GeneSetEnrichmentAnalysisWiki - User contributions [en] https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Special:Contributions/18.103.13.107 User contributions en MediaWiki 1.34.4 Fri, 29 Mar 2024 00:13:51 GMT Gsea Citation https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_Citation&diff=1717 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_Citation&diff=1717 <p>18.103.13.107: </p> <hr /> <div>&lt;p class=&quot;MsoNormal&quot;&gt;Please cite the elements of GSEA that you have used in your research.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/span&gt;For the gene set enrichment analysis: the analysis was first reported in Mootha et al, the Kolmogorov-Smirnov statistic was first used in the context of a set of genes in Lamb et al, and a full mathematical description of the GSEA methodology is provided in Subramanian, Tamayo, et al. To cite the gene set enrichment analysis, you may want to reference one or more these papers: &lt;/p&gt;<br /> &lt;div style=&quot;font-family: arial; margin-left: 40px;&quot;&gt;<br /> &lt;p&gt;&lt;span style=&quot;font-size: 9pt;&quot;&gt;Mootha, V. K., C. M. Lindgren, et al. (2003). &lt;span style=&quot;font-weight: bold;&quot;&gt;PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.&lt;/span&gt; Nat Genet 34(3): 267-73.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p&gt;&lt;span style=&quot;font-size: 9pt;&quot;&gt;Lamb, J., Ramaswamy, S., Ford, H. L., Contreras, B., Martinez, R. V., Kittrell, F. S., Zahnow, C. A., Patterson, N., Golub, T. R. &amp;amp; Ewen, M. E. (2003). &lt;/span&gt;&lt;strong&gt;A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer.&lt;/strong&gt;&lt;span style=&quot;font-size: 9pt;&quot;&gt; Cell 114, 323&amp;ndash;334.&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. &amp;amp; Mesirov, J. P. (2005)&amp;nbsp;&lt;strong&gt;&lt;strong&gt;Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. &lt;/strong&gt;&lt;/strong&gt;Proc. Natl. Acad. Sci. USA 102, 15545-15550.&lt;strong&gt; &lt;/strong&gt; &lt;/p&gt;<br /> &lt;/div&gt;<br /> &lt;div style=&quot;font-family: arial; margin-left: 40px;&quot;&gt; &lt;/div&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;To cite the Molecular Signature Database (MSigDB), whether used with GSEA or another type of analysis, please specify the MSigDB version used in your analysis and the paper that describes it. For example:&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;Molecular Signature Database (MSigDB), May 2006 release&lt;br /&gt;--BMC paper to be released--&lt;br /&gt;&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Note&lt;/span&gt;: For MSigDB releases prior to May 2006, please cite Subramanian, Tamayo, et al. (as listed above).&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/span&gt;To cite the C3 (motif) gene sets, please reference Xie et al, as well as the Molecular Signature Database (MSigDB), as described above. For example:&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander &amp;amp; Manolis Kellis. &lt;strong style=&quot;&quot;&gt;Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals&lt;/strong&gt;. Nature 434, 17 March 2005.&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;Molecular Signature Database (MSigDB), May 2006 release&lt;br /&gt;--BMC paper to be released--&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;To cite specific MSigDB gene sets, please reference the original paper on which the gene set was based, as listed in the Gene Set Card, as well as the MSigDB, as described above. For example, to cite the curated gene set ADIP_VS_PREADIP_UP:&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;Gerhold DL, Liu F, Jiang G, Li Z, Xu J, Lu M, Sachs JR, Bagchi A, Fridman A, Holder DJ, Doebber TW, Berger J, Elbrecht A, Moller DE, Zhang BB. &lt;strong style=&quot;&quot;&gt;Gene expression profile of adipocyte differentiation and its regulation by peroxisome proliferator-activated receptor-gamma agonists. &lt;/strong&gt;Endocrinology&lt;strong style=&quot;&quot;&gt; &lt;/strong&gt;2002 Jun;143(6):2106-18.&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;Molecular Signature Database (MSigDB), May 2006 release&lt;br /&gt;--BMC paper to be released--&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/span&gt;To cite the GSEA software, either GSEA-P or GSEA-R, please reference the GSEA web site (http://www.broad.mit.edu/gsea/) and the Application Note paper. For example:&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;GSEA-P software (&lt;a href=&quot;http://www.broad.mit.edu/gsea&quot;&gt;http://www.broad.mit.edu/gsea&lt;/a&gt;)&lt;br /&gt;--Application Note paper to be released--&lt;br /&gt;&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Note: &lt;/span&gt;Until the Application Note paper is released, please cite the URL.&lt;br /&gt;&lt;/p&gt;</div> Tue, 11 Apr 2006 19:10:34 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_Citation Gsea enhancements https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1702 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1702 <p>18.103.13.107: </p> <hr /> <div>&lt;span style=&quot;font-weight: bold;&quot;&gt;GSEA Beta 4/7:&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. software_download.html: easilly -&amp;gt; easily. Might also want to add: If you cannot remember the location of the GSEA home folder, start the application and click &amp;quot;Help&amp;gt;Show GSEA Home Folder&amp;quot;.&lt;br /&gt;&lt;br /&gt;2. No uninstall directory in GSEA home folder.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;On the GSEA Web Site:&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. Doc page top menu has a different order than other pages:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; Other:&amp;nbsp; Home&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Software&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; MSigDB&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; GeneSetCards&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Documentation&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Resources&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; Doc:&amp;nbsp;&amp;nbsp;&amp;nbsp; Home&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Documentation&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Software&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; MSigDB&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; GeneSetCards&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Resources&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;2. GSEA icon on doc page should link to GSEA home page (not doc page)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Unable to fix&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. MSigDB page needs to point to license notice, as on V1 web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;4. Are we putting Java docs for GSEA application on the web site? Where are they?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Probably not unless someone asks&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;5. Make the Contact Us page more prominent (add it to Resources page?). &lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;6. On the Contact Us page, software credits and MSigDB credits should point to the appropriate wiki pages.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;7. How should people cite GSEA and/or MSigDB in their papers (eg I used GSEA with my own gene set or the p53 gene set is enriched in my analysis)? We need to add this info to the Publications page (and to MSigDB page?).&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;See email&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;8. On the software download page (http://wwwdev.broad.mit.edu/gsea/software/software_download.html), incorrect link to GSEA-R zip file.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;9. The title bar on the Gene Set Card pages is missing the GSEA logo and has the menu items in the wrong order (Doc before Software rather than before Resources). Since I notice that you've already fixed many of the above, perhaps it's just that I was looking while you were playing with the pages?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Next build will fix this &lt;/span&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Found 4/4:&lt;/span&gt;&lt;br /&gt;1. Specify Bhattacharyya with Continous pheno, should get error 1011 (get hardcoded error). &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Bhattacharyya is a continuous metric so isnt this correct?&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;When I run &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Bhattacharyya with a continuous phenotype I get the following error (no error help button):&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;Tool execution error&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;Message: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;This metric can only be used with 2 class comparisons&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;-------------------------------------------------------------&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;java.lang.RuntimeException: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;This metric can only be used with 2 class comparisons&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at edu.mit.broad.genome.alg.VectorSplitter._barf_not_biphasic(VectorSplitter.java:71)....&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Specify Pearson with Categorical, should get error 1010 (get hardcoded error). &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Pearson is allowed for categorical &amp;amp; continuous&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;When I run Pearson with a Categorical phenotype, I get the following error (no help button); now that I look more closely, it doesn't seem to be related to the Categorical/Continuous thing...&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Message: For input string: &amp;quot;MUT&amp;quot;&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;-------------------------------------------------------------&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;java.lang.NumberFormatException: For input string: &amp;quot;MUT&amp;quot;&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.lang.Float.parseFloat(Unknown Source)....&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;3. Add Fold Change back into &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter drop-down list.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;. Its called 'Ratio_of_Means' to be more prcise on what fold change is.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found 4/3 (Aravind's notes from Heidi's cube):&lt;/span&gt;&lt;/span&gt;&lt;br style=&quot;font-weight: bold;&quot; /&gt;&lt;br /&gt;tool cache doesnt show up&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;tool cache wrong on errored out report&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;file chooser static&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;No fix. Known limitation&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;installer must install databases/Hs.alias&lt;br /&gt;installer must delete folder&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Made new software upgrade to v2 page&lt;/span&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;Found 4/3 with new build:&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;1. Attempt to run the leading edge analysis gives following error (Build HTML Report works fine): &lt;br /&gt;java.lang.NoClassDefFoundError: org/apache/commons/math/MathException&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeAnalysis.&amp;lt;init&amp;gt;(LeadingEdgeAnalysis.java:127)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.runAnalysis(LeadingEdgeWidget.java:341)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.access$400(LeadingEdgeWidget.java:59)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget$4.run(LeadingEdgeWidget.java:313)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.AbstractWorkerThread$2.run(AbstractWorkerThread.java:49)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.security.AccessController.doPrivileged(Native Method)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.AbstractWorkerThread.runTask(AbstractWorkerThread.java:45)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.workers.DefaultWorkerThread.run(DefaultWorkerThread.java:153)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.lang.Thread.run(Unknown Source)&lt;br /&gt;&lt;br /&gt;Message: na&lt;br /&gt;-------------------------------------------------------------&lt;br /&gt;java.lang.Throwable: na&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at edu.mit.broad.xbench.core.api.AbstractWindowManager.showError(AbstractWindowManager.java:72)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.XToolsMessageHandler.showErrorDialog(XToolsMessageHandler.java:33)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.uiutil.UIUtil.showErrorDialog(UIUtil.java:41)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.runAnalysis(LeadingEdgeWidget.java:327)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.access$000(LeadingEdgeWidget.java:59)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget$1.actionPerformed(LeadingEdgeWidget.java:129)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.DefaultButtonModel.setPressed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.JComponent.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.processEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.processEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Window.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventQueue.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEvents(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEvents(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.run(Unknown Source)&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;Notes from user tests 3/31&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;Needs java1.5&lt;br /&gt;So if you launch on a mac and see the error message unsupported class version it means that your mac (or windows) doesnt not have the correct java version.&lt;br /&gt;For the mac: http://docs.info.apple.com/article.html?artnum=302412&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;8&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer includes HTML report option&lt;br /&gt;2. Installer works: Download new version from: &lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;XXX&lt;/span&gt;&lt;br /&gt;3. New msigdb xml file and gene set cards created. Gene set descriptions cleaned up. Anything odd is now a bug.&lt;br /&gt;4. I'll be adding to the software version 2 release notes wiki page (pl subscribe and edit as needed).&lt;br /&gt;5. Unified application messages (they are all now in the status bar at the bottom), no more system console viewer&lt;br /&gt;6. Added a splash screen so that users know the application is loading after its desktop application has been double clicked&lt;br /&gt;7. Implemented the startup screen (let me know what you think of its content)&lt;br /&gt;8. For the chip platform parameter, multiple chips can be selected (for example if a dataset is made from 2 different chips). &lt;br /&gt;9. By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/27 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. From the Load Data page: load a gene set matrix, use Extract Gene Sets to create gene sets in memory, use Create Ranked List to create a ranked list from one of those gene sets. It tells me that it created the ranked list and gives me the following info messages, but I can't find the ranked list: it's not in the default output folder, the object cache list, or the drop-downs on the PreRanked GSEA page. &lt;br /&gt;&lt;br /&gt;1355 [INFO ] Starting: =&amp;gt; Extract GeneSets from the GeneMatrix&lt;br /&gt;1385 [INFO ] Successfully created a GeneSet from the Dataset s2_gene_set_database.diabetes.gmt into: 323 gene sets&lt;br /&gt;1425 [INFO ] Null widget - no window opened&lt;br /&gt;9346 [INFO ] Starting: =&amp;gt; Create a RankedList&lt;br /&gt;9366 [INFO ] Successfully created a RankedList from the GeneSet 41BBPATHWAY into: 34 members&lt;br /&gt;9366 [INFO ] Null widget - no window opened&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;I fixed this but then rmoved the action - because i wondered if converting a gene set to a ranked list would cause confusion b/w what a gene set is and what a ranked list is. Thoughts?&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Agreed; I removed it from the doc.&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;/span&gt;&lt;br /&gt;2. On the Leading Edge Report page, I built a report, realized I built the wrong one, so selected and built a different one. A new tab appears, but it doesn't get the focus (so I didn't notice it at first). Also, the tabs that get created should have close (X) icons.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Pl ask Josh; &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;sent him email&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. The output folder creates a subfolder for each day (mar21, mar22, etc). Shouldn't the folder name include the year? Or, do we expect people to be deleting the reports on a regular basis?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Good point. But folder names are key to a lot of things and i'm wary of changing the convention at this stage.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Sounds reasonable. We can decide whether to change it or doc it in the next release (doc=recommend that people periodically delete old reports, renaming and saving what they want to keep).&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On the Run GSEA page, select phenotypes, on the Select one or more phenotypes window, the button should be Create &lt;span style=&quot;text-decoration: underline;&quot;&gt;an &lt;/span&gt;on-the-fly phenotype... rather than Create &lt;span style=&quot;text-decoration: underline;&quot;&gt;a &lt;/span&gt;on-the-fly phenotype.... &lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/24 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. Names generaed by GSEA were too long for Windows. My personal profile failed to load and I was logged in with a temporary. Had to zip (and delete) one of my GSEA report folders before I could log into Windows with my own profile. Put the zipped reports folder in dropbox/foraravind.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;IMPortant to fix. &lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Is this impossible to fix or important to fix?&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;Found/requested 3/22 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt; &lt;/span&gt;&lt;/span&gt;But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Indeed, if you set chip once for a dataset, the program remembers this association during the current session.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed (note: it was clumsy to place a desc text in the table as it could be very long. So, the 2 modes are: 1) na in the desc field of the gmx /gmt file -&amp;gt; auto links to msigdb. 2) a valid url i.e text that starts with http &amp;gt; links to the custom http ... site specified&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc with file formats.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;This is a 'feature'. The object cache lists the programs memory&amp;nbsp; while the leading edge cache lists the file system - i.e all analysis ever done (which could be too large to load into memory).&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed (new gene sets database)&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;6. Analysis History page still isn't showing up for me. &lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;9. On the Algorithms page of the Preferences window, delete the phrase &amp;quot;(they can also be changed in params)&amp;quot; -- only one of them can.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;10. Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; 11. On the GSEA analysis report:&amp;nbsp; Indent the phenotype permutation warning (or make it another bullet) so it looks more like part of the &amp;quot;Other&amp;quot; section. Also, remove the message at the&amp;nbsp; bottom: &amp;quot;# of genesets before size filtering: 3 and # of genesets after size filtering: 3&amp;quot; (that info is already in the &amp;quot;Gene set details&amp;quot; section of the report).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;12. Leading Edge Viewer looks good! Two things: (1) The bottom two viewers have zoom controlled by CTRL+[ and CTRL+], but I can't get the focus to the right-hand viewer. The CTRL sequence always zooms the left viewer.&amp;nbsp; (2) The viewers completely replace the old HTML report, which included the details of gene sets used (name, # of members, # of members in signal, tag%, list%, signal strength). That info seems useful and now lost? (The 2nd viewer (the set-to-set comparison) has a nice open spot for a &amp;quot;Display gene set details&amp;quot; button...)&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Josh is adding 2) and can help fix 1). &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;sent email&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;1&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer&lt;br /&gt;2. Added a preferences field for path to user home dir.&lt;br /&gt;3. made native the default space in gsea. Not sure if this is better??&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt; I prefer gene_symbol since that's what we recommend. &lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;4. default collection of gene sets available via ftp&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/17:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Add Command button to Leading Edge page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Cant do this easilly because of the way the command thing is setup.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;You said you could do this after all.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Na anymore because of Joshs improved interactive impl&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Leading edge from command line give me fatal errors:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases&amp;nbsp;&amp;nbsp;&amp;nbsp; at &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip&amp;nbsp;&amp;nbsp;&amp;nbsp; at&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 799&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo&amp;nbsp;&amp;nbsp;&amp;nbsp; at&lt;br /&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&lt;br /&gt;Must set -DGSEA=true flag&lt;br /&gt;So,&lt;br /&gt;&lt;br /&gt; &lt;pre&gt;java -Xmx ... -DGSEA=true xtools.....&lt;/pre&gt; &lt;br /&gt;&lt;br /&gt;3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; Find sets that contain this gene page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 153, 0);&quot;&gt;Joshs reworked impl will replace this and the export option should be added to it&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On Run GSEA, change parameter name from &amp;quot;Analyze in the feature space&amp;quot; to &amp;quot;Gene/probe identifier format&amp;quot;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Lets talk. &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Forgot to bring this up in our last chat.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;What about using &amp;quot;Collapse dataset&amp;quot; as the name, where values are True (use 'chip' to collapse dataset to gene symbols) and False (blah blah).&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;5. Remove Downloads&amp;gt;Download Gene Sets (no longer needed now that we have MSigDB page).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;6. Change first two Help items to &amp;quot;GSEA web site&amp;quot; and &amp;quot;GSEA documentation&amp;quot;. First points to home page of web site and&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; second points to the doc page of the web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Bugs found 3/15/2006 include:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Generate a report, go to &amp;quot;Other&amp;quot; section, look at parameters. Error, file cannot be found.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;.&lt;br /&gt;&lt;br /&gt;2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.&lt;/span&gt;</div> Fri, 07 Apr 2006 12:59:19 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_enhancements Gsea enhancements https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1700 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1700 <p>18.103.13.107: </p> <hr /> <div>&lt;span style=&quot;font-weight: bold;&quot;&gt;On the GSEA Web Site (Beta) 4/7:&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. software_download.html: easilly -&amp;gt; easily&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;On the GSEA Web Site:&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. Doc page top menu has a different order than other pages:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; Other:&amp;nbsp; Home&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Software&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; MSigDB&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; GeneSetCards&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Documentation&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; Resources&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; Doc:&amp;nbsp;&amp;nbsp;&amp;nbsp; Home&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Documentation&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Software&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; MSigDB&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; GeneSetCards&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp; Resources&amp;nbsp; &amp;circ;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;2. GSEA icon on doc page should link to GSEA home page (not doc page)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Unable to fix&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. MSigDB page needs to point to license notice, as on V1 web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;4. Are we putting Java docs for GSEA application on the web site? Where are they?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Probably not unless someone asks&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;5. Make the Contact Us page more prominent (add it to Resources page?). &lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;6. On the Contact Us page, software credits and MSigDB credits should point to the appropriate wiki pages.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;7. How should people cite GSEA and/or MSigDB in their papers (eg I used GSEA with my own gene set or the p53 gene set is enriched in my analysis)? We need to add this info to the Publications page (and to MSigDB page?).&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;See email&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;8. On the software download page (http://wwwdev.broad.mit.edu/gsea/software/software_download.html), incorrect link to GSEA-R zip file.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;9. The title bar on the Gene Set Card pages is missing the GSEA logo and has the menu items in the wrong order (Doc before Software rather than before Resources). Since I notice that you've already fixed many of the above, perhaps it's just that I was looking while you were playing with the pages?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Next build will fix this &lt;/span&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Found 4/4:&lt;/span&gt;&lt;br /&gt;1. Specify Bhattacharyya with Continous pheno, should get error 1011 (get hardcoded error). &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Bhattacharyya is a continuous metric so isnt this correct?&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;When I run &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Bhattacharyya with a continuous phenotype I get the following error (no error help button):&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;Tool execution error&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;Message: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;This metric can only be used with 2 class comparisons&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;-------------------------------------------------------------&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;java.lang.RuntimeException: Template is not biphasic. Name: 100_g_at_profile_in_p53_dataset_hgu95av2.cls#100_g_at # splits= 50&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;This metric can only be used with 2 class comparisons&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at edu.mit.broad.genome.alg.VectorSplitter._barf_not_biphasic(VectorSplitter.java:71)....&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Specify Pearson with Categorical, should get error 1010 (get hardcoded error). &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Pearson is allowed for categorical &amp;amp; continuous&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;When I run Pearson with a Categorical phenotype, I get the following error (no help button); now that I look more closely, it doesn't seem to be related to the Categorical/Continuous thing...&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Message: For input string: &amp;quot;MUT&amp;quot;&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;-------------------------------------------------------------&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;java.lang.NumberFormatException: For input string: &amp;quot;MUT&amp;quot;&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.lang.Float.parseFloat(Unknown Source)....&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;3. Add Fold Change back into &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes&lt;/span&gt; parameter drop-down list.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;. Its called 'Ratio_of_Means' to be more prcise on what fold change is.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found 4/3 (Aravind's notes from Heidi's cube):&lt;/span&gt;&lt;/span&gt;&lt;br style=&quot;font-weight: bold;&quot; /&gt;&lt;br /&gt;tool cache doesnt show up&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;tool cache wrong on errored out report&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;file chooser static&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;No fix. Known limitation&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;installer must install databases/Hs.alias&lt;br /&gt;installer must delete folder&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Made new software upgrade to v2 page&lt;/span&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;Found 4/3 with new build:&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;1. Attempt to run the leading edge analysis gives following error (Build HTML Report works fine): &lt;br /&gt;java.lang.NoClassDefFoundError: org/apache/commons/math/MathException&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeAnalysis.&amp;lt;init&amp;gt;(LeadingEdgeAnalysis.java:127)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.runAnalysis(LeadingEdgeWidget.java:341)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.access$400(LeadingEdgeWidget.java:59)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget$4.run(LeadingEdgeWidget.java:313)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.AbstractWorkerThread$2.run(AbstractWorkerThread.java:49)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.security.AccessController.doPrivileged(Native Method)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.AbstractWorkerThread.runTask(AbstractWorkerThread.java:45)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at foxtrot.workers.DefaultWorkerThread.run(DefaultWorkerThread.java:153)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.lang.Thread.run(Unknown Source)&lt;br /&gt;&lt;br /&gt;Message: na&lt;br /&gt;-------------------------------------------------------------&lt;br /&gt;java.lang.Throwable: na&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at edu.mit.broad.xbench.core.api.AbstractWindowManager.showError(AbstractWindowManager.java:72)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.XToolsMessageHandler.showErrorDialog(XToolsMessageHandler.java:33)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.uiutil.UIUtil.showErrorDialog(UIUtil.java:41)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.runAnalysis(LeadingEdgeWidget.java:327)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget.access$000(LeadingEdgeWidget.java:59)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at org.genepattern.gsea.LeadingEdgeWidget$1.actionPerformed(LeadingEdgeWidget.java:129)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.DefaultButtonModel.setPressed(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at javax.swing.JComponent.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.processEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.processEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Container.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Window.dispatchEventImpl(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.Component.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventQueue.dispatchEvent(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEvents(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.pumpEvents(Unknown Source)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; at java.awt.EventDispatchThread.run(Unknown Source)&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;Notes from user tests 3/31&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;Needs java1.5&lt;br /&gt;So if you launch on a mac and see the error message unsupported class version it means that your mac (or windows) doesnt not have the correct java version.&lt;br /&gt;For the mac: http://docs.info.apple.com/article.html?artnum=302412&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;8&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer includes HTML report option&lt;br /&gt;2. Installer works: Download new version from: &lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;XXX&lt;/span&gt;&lt;br /&gt;3. New msigdb xml file and gene set cards created. Gene set descriptions cleaned up. Anything odd is now a bug.&lt;br /&gt;4. I'll be adding to the software version 2 release notes wiki page (pl subscribe and edit as needed).&lt;br /&gt;5. Unified application messages (they are all now in the status bar at the bottom), no more system console viewer&lt;br /&gt;6. Added a splash screen so that users know the application is loading after its desktop application has been double clicked&lt;br /&gt;7. Implemented the startup screen (let me know what you think of its content)&lt;br /&gt;8. For the chip platform parameter, multiple chips can be selected (for example if a dataset is made from 2 different chips). &lt;br /&gt;9. By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/27 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. From the Load Data page: load a gene set matrix, use Extract Gene Sets to create gene sets in memory, use Create Ranked List to create a ranked list from one of those gene sets. It tells me that it created the ranked list and gives me the following info messages, but I can't find the ranked list: it's not in the default output folder, the object cache list, or the drop-downs on the PreRanked GSEA page. &lt;br /&gt;&lt;br /&gt;1355 [INFO ] Starting: =&amp;gt; Extract GeneSets from the GeneMatrix&lt;br /&gt;1385 [INFO ] Successfully created a GeneSet from the Dataset s2_gene_set_database.diabetes.gmt into: 323 gene sets&lt;br /&gt;1425 [INFO ] Null widget - no window opened&lt;br /&gt;9346 [INFO ] Starting: =&amp;gt; Create a RankedList&lt;br /&gt;9366 [INFO ] Successfully created a RankedList from the GeneSet 41BBPATHWAY into: 34 members&lt;br /&gt;9366 [INFO ] Null widget - no window opened&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;I fixed this but then rmoved the action - because i wondered if converting a gene set to a ranked list would cause confusion b/w what a gene set is and what a ranked list is. Thoughts?&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Agreed; I removed it from the doc.&lt;/span&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;/span&gt;&lt;br /&gt;2. On the Leading Edge Report page, I built a report, realized I built the wrong one, so selected and built a different one. A new tab appears, but it doesn't get the focus (so I didn't notice it at first). Also, the tabs that get created should have close (X) icons.&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Pl ask Josh; &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;sent him email&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. The output folder creates a subfolder for each day (mar21, mar22, etc). Shouldn't the folder name include the year? Or, do we expect people to be deleting the reports on a regular basis?&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Good point. But folder names are key to a lot of things and i'm wary of changing the convention at this stage.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Sounds reasonable. We can decide whether to change it or doc it in the next release (doc=recommend that people periodically delete old reports, renaming and saving what they want to keep).&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On the Run GSEA page, select phenotypes, on the Select one or more phenotypes window, the button should be Create &lt;span style=&quot;text-decoration: underline;&quot;&gt;an &lt;/span&gt;on-the-fly phenotype... rather than Create &lt;span style=&quot;text-decoration: underline;&quot;&gt;a &lt;/span&gt;on-the-fly phenotype.... &lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/24 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. Names generaed by GSEA were too long for Windows. My personal profile failed to load and I was logged in with a temporary. Had to zip (and delete) one of my GSEA report folders before I could log into Windows with my own profile. Put the zipped reports folder in dropbox/foraravind.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 0, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;IMPortant to fix. &lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Is this impossible to fix or important to fix?&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;Found/requested 3/22 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt; &lt;/span&gt;&lt;/span&gt;But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Indeed, if you set chip once for a dataset, the program remembers this association during the current session.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed (note: it was clumsy to place a desc text in the table as it could be very long. So, the 2 modes are: 1) na in the desc field of the gmx /gmt file -&amp;gt; auto links to msigdb. 2) a valid url i.e text that starts with http &amp;gt; links to the custom http ... site specified&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc with file formats.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;This is a 'feature'. The object cache lists the programs memory&amp;nbsp; while the leading edge cache lists the file system - i.e all analysis ever done (which could be too large to load into memory).&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed (new gene sets database)&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;6. Analysis History page still isn't showing up for me. &lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;9. On the Algorithms page of the Preferences window, delete the phrase &amp;quot;(they can also be changed in params)&amp;quot; -- only one of them can.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;10. Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; 11. On the GSEA analysis report:&amp;nbsp; Indent the phenotype permutation warning (or make it another bullet) so it looks more like part of the &amp;quot;Other&amp;quot; section. Also, remove the message at the&amp;nbsp; bottom: &amp;quot;# of genesets before size filtering: 3 and # of genesets after size filtering: 3&amp;quot; (that info is already in the &amp;quot;Gene set details&amp;quot; section of the report).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;12. Leading Edge Viewer looks good! Two things: (1) The bottom two viewers have zoom controlled by CTRL+[ and CTRL+], but I can't get the focus to the right-hand viewer. The CTRL sequence always zooms the left viewer.&amp;nbsp; (2) The viewers completely replace the old HTML report, which included the details of gene sets used (name, # of members, # of members in signal, tag%, list%, signal strength). That info seems useful and now lost? (The 2nd viewer (the set-to-set comparison) has a nice open spot for a &amp;quot;Display gene set details&amp;quot; button...)&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Josh is adding 2) and can help fix 1). &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;sent email&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;1&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer&lt;br /&gt;2. Added a preferences field for path to user home dir.&lt;br /&gt;3. made native the default space in gsea. Not sure if this is better??&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt; I prefer gene_symbol since that's what we recommend. &lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;4. default collection of gene sets available via ftp&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/17:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Add Command button to Leading Edge page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Cant do this easilly because of the way the command thing is setup.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;You said you could do this after all.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Na anymore because of Joshs improved interactive impl&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Leading edge from command line give me fatal errors:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases&amp;nbsp;&amp;nbsp;&amp;nbsp; at &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip&amp;nbsp;&amp;nbsp;&amp;nbsp; at&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 799&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo&amp;nbsp;&amp;nbsp;&amp;nbsp; at&lt;br /&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&lt;br /&gt;Must set -DGSEA=true flag&lt;br /&gt;So,&lt;br /&gt;&lt;br /&gt; &lt;pre&gt;java -Xmx ... -DGSEA=true xtools.....&lt;/pre&gt; &lt;br /&gt;&lt;br /&gt;3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; Find sets that contain this gene page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 153, 0);&quot;&gt;Joshs reworked impl will replace this and the export option should be added to it&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On Run GSEA, change parameter name from &amp;quot;Analyze in the feature space&amp;quot; to &amp;quot;Gene/probe identifier format&amp;quot;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Lets talk. &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Forgot to bring this up in our last chat.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;What about using &amp;quot;Collapse dataset&amp;quot; as the name, where values are True (use 'chip' to collapse dataset to gene symbols) and False (blah blah).&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;5. Remove Downloads&amp;gt;Download Gene Sets (no longer needed now that we have MSigDB page).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;6. Change first two Help items to &amp;quot;GSEA web site&amp;quot; and &amp;quot;GSEA documentation&amp;quot;. First points to home page of web site and&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; second points to the doc page of the web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done &lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Doc'd&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Bugs found 3/15/2006 include:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Generate a report, go to &amp;quot;Other&amp;quot; section, look at parameters. Error, file cannot be found.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;.&lt;br /&gt;&lt;br /&gt;2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.&lt;br /&gt;&lt;br style=&quot;color: rgb(255, 102, 0);&quot; /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.&lt;/span&gt;</div> Fri, 07 Apr 2006 12:25:59 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_enhancements Quick reference https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Quick_reference&diff=1606 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Quick_reference&diff=1606 <p>18.103.13.107: </p> <hr /> <div>&lt;br /&gt;For descriptions of the GSEA windows and menu bar, use the following links. &lt;br /&gt;These are the help pages displayed when you click a help button in the GSEA application.&lt;br /&gt;&lt;br /&gt;Menu bar: &lt;br /&gt;GSEA main window: &lt;br /&gt;Load Data page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Load_Data_Page]&lt;br /&gt;Run GSEA page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Run_GSEA_Page]&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; Select One or More Phenotypes: &lt;br /&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Select_One_or_More_Phenotypes_Windo]&lt;br /&gt;Leading Edge Analysis page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Leading_Edge_Analysis_Page]&lt;br /&gt;Chip-to-Chip page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Chip2Chip_Page]&lt;br /&gt;Browse MSigDB page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Browse_MsigDB_Page]&lt;br /&gt;Analysis History page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Analysis_History_Page]&lt;br /&gt;GSEA Preranked page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_GSEAPreranked_Page]&lt;br /&gt;Collapse Dataset page: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_CollapseDataset_Page]&lt;br /&gt;Preferences window: [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#_Preferences_Window]</div> Fri, 31 Mar 2006 18:18:45 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Quick_reference Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1528 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1528 <p>18.103.13.107: </p> <hr /> <div>&lt;br /&gt;<br /> &lt;h3&gt;Documentation Home&lt;/h3&gt;<br /> Welcome to the GSEA documentation page!&lt;br /&gt;&lt;br /&gt;For information about GSEA, click the links in the navigation bar to the left.&lt;br /&gt;&lt;br /&gt;If you have comments, suggestions, or cannot find the information that you need, please let us know: mailto:gsea@broad.mit.edu.&lt;br /&gt;&lt;br /&gt;<br /> &lt;h3&gt;User Guide&lt;/h3&gt;<br /> The GSEA User Guide is provided in HTML and PDF formats:&lt;br /&gt;&lt;br /&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm GSEAUserGuide.htm]&lt;br /&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEA/GSEAUserGuide.pdf GSEAUserGuide.pdf]</div> Tue, 28 Mar 2006 18:25:11 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Data formats https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Data_formats&diff=1508 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Data_formats&diff=1508 <p>18.103.13.107: </p> <hr /> <div>&lt;h1&gt;&lt;a name=&quot;_Toc127331825&quot;&gt;Data Formats Supported by GSEA&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p&gt;&lt;span style=&quot;&quot;&gt;For sample files, see [http://wwwdev.broad.mit.edu/gsea/resources/datasets_index.html http://wwwdev.broad.mit.edu/gsea/resources/datasets_index.html] or, from within GSEA, select &lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;Help&amp;gt;Show GSEA Home Folder&lt;/span&gt;&lt;/code&gt; and go to the &lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;examples&lt;/span&gt;&lt;/code&gt; subfolder.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;&lt;span style=&quot;font-size: 14pt;&quot;&gt;Expression data formats&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_GCT_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;GCT: Gene Cluster Text file format (*.gct)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_RES_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;RES: ExpRESsion (with P and A calls) file format (*.res)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_PCL_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;PCL: Stanford cDNA file format (*.pcl)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;Note&lt;/strong&gt;: The GCT &amp;amp; RES expression formats supported by GSEA are identical to those supported by GenePattern.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;&lt;span style=&quot;font-size: 14pt;&quot;&gt;Phenotype data formats&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_CLS_File_Format:_Categorical&quot;&gt;&lt;span style=&quot;&quot;&gt;CLS: Categorical (e.g tumor vs normal) class file format (*.cls)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_CLS_File_Format:_Continuous&quot;&gt;&lt;span style=&quot;&quot;&gt;CLS: Continuous (e.g time-series or gene profile) file format (*.cls)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;&lt;span style=&quot;font-size: 14pt;&quot;&gt;Gene set database formats&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_GMX_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;GMX: Gene MatriX file format (*.gmx)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_GMT_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;GMT: Gene Matrix Transposed file format (*.gmt)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_GRP_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;GRP: Gene set file format (*.grp)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_MDB_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;MDB: Molecular signature database file format (*.mdb)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;Note&lt;/strong&gt;: Typically, you use the GMX or GMT formats to define gene sets.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;&lt;span style=&quot;font-size: 14pt;&quot;&gt;Microarray annotation formats&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_CHIP_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;CHIP: Chip file format (*.chip)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_CSV_File_Format_(for Chip Files)&quot;&gt;&lt;span style=&quot;&quot;&gt;CSV: Comma Separated Version (*.csv)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong style=&quot;&quot;&gt;&lt;span style=&quot;font-size: 14pt;&quot;&gt;Ranked gene lists&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;a href=&quot;#_RNK_File_Format&quot;&gt;&lt;span style=&quot;&quot;&gt;RNK: Ranked list file format (*.rnk)&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_GCT:_Gene_Cluster_Text file format &quot;&gt;&lt;/a&gt;&lt;a name=&quot;_GCT_File_Format&quot;&gt;&lt;/a&gt;GCT File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The GCT format is a tab delimited file format that describes an expression dataset. It is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: gct_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;first line&lt;/strong&gt; contains the version string and is always the same for this file format. Therefore, the first line must be as follows: &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;#1.2 &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;second line&lt;/strong&gt; contains numbers indicating the size of the data table that is contained in the remainder of the file. Note that the name and description columns are not included in the number of data columns. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;(&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;# of data rows) (tab) (# of data columns)&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;7129 58 &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;third line&lt;/strong&gt; contains a list of identifiers for the samples associated with each of the columns in the remainder of the file. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;Name(tab)Description(tab)(sample 1 name)(tab)(sample 2 name) (tab) ... (sample N name) &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt; &lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;Name Description DLBC1_1 DLBC2_1 ... DLBC58_0 &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;remainder&lt;/strong&gt; of the data file contains data for each of the genes. There is one line for each gene and one column for each of the samples. The first two fields in the line contain name and descriptions for the genes (names and descriptions can contain spaces since fields are separated by tabs). The number of lines should agree with the number of data rows specified on line 2. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(gene name) (tab) (gene description) (tab) (col 1 data) (tab) (col 2 data) (tab) ... (col N data) &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt; &lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;AFFX-BioB-5_at AFFX-BioB-5_at (endogenous control) -104 -152 -158 ... -44 &lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_RES_File_Format&quot;&gt;&lt;/a&gt;RES File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The RES file format is a tab delimited file format that describes an expression dataset. It is organized as follows. The main difference between RES and GCT file formats is the RES file format contains labels for each gene's absent (A) versus present (P) calls as generated by Affymetrix's GeneChip software.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: res_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;first line&lt;/strong&gt; contains a list of labels identifying the samples associated with each of the columns in the remainder of the file. Two tabs (\t\t) separate the sample identifier labels because each sample contains two data values (an expression value and a present/marginal/absent call). &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;Description (tab) Accession (tab) (sample 1 name) (tab) (tab) (sample 2 name) (tab) (tab) ... (sample N name)&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;For example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;Description Accession DLBC1_1 DLBC2_1 ... DLBC58_0&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;second line&lt;/strong&gt; contains a list of sample descriptions. Currently, GSEA ignores these descriptions. Our RES file creation tool places the sample data file name and scale factors in this row, as shown below.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(tab) (sample 1 description) (tab) (tab) (sample 2 description) (tab) (tab) ... (sample N description) &lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;MG2000062219AA MG2000062256AA/scale factor=1.2172 ... MG2000062211AA/scale factor=1.1214&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;third line&lt;/strong&gt; contains a number indicating the number of rows in the data table that is contained in the remainder of the file. Note that the name and description columns are not included in the number of data columns. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(# of data rows)&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;For example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;7129&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;remainder&lt;/strong&gt; of the data file contains data for each of the genes. There is one row for each gene and two columns for each of the samples. The first two fields in the row contain the description and name for each of the genes (names and descriptions can contain spaces since fields are separated by tabs). The description field is optional but the tab following it is not. Each sample has two pieces of data associated with it: an expression value and an associated Absent/Marginal/Present (A/M/P) call. The A/M/P calls are generated by microarray scanning software (such as Affymetrix's GeneChip software) and are an indication of the confidence in the measured expression value. Currently, GSEA ignores the Absent/Marginal/Present call. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(gene description) (tab) (gene name) (tab) (sample 1 data) (tab) (sample 1 A/P call) (tab) (sample 2 data) (tab) (sample 2 A/P call) (tab) ... (sample N data) (tab) (sample N A/P call) &lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;For example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;AFFX-BioB-5_at (endogenous control) AFFX-BioB-5_at -104 A -152 A ... -44 A&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_PCL_File_Format&quot;&gt;&lt;/a&gt;PCL File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The PCL file format is a tab delimited file format that describes an expression dataset. It is organized as follows. Support for this format is provided because several Stanford cDNA datasets are available in the PCL format. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: pcl_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_CLS_File_Format:_Categorical&quot;&gt;&lt;/a&gt;CLS File Format: Categorical&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CLS file format defines phenotype (class or template) labels and associates each sample in the expression data with a label. The CLS file format uses spaces or tabs to separate the fields.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CLS file format differs somewhat depending on whether you are defining categorical or continuous phenotypes. Categorical labels define discrete phenotypes; for example, normal vs tumor). For categorical labels, the CLS file format is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: cls_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;first line&lt;/strong&gt; of a CLS file contains numbers indicating the number of samples and number of classes. The number of samples should correspond to the number of samples in the associated RES or GCT data file. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(number of samples) (space) (number of classes) (space) 1 &lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;58 2 1 &lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;second line&lt;/strong&gt; in a CLS file contains names for the class numbers. The line should begin with a pound sign (#) followed by a space. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;# (space) (class 0 name) (space) (class 1 name)&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;For example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;# cured fatal/ref&lt;/span&gt;&lt;/code&gt; &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The &lt;strong style=&quot;&quot;&gt;third line&lt;/strong&gt; contains numeric class labels for each of the samples. The number of class labels should be the same as the number of samples specified in the first line.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;Line format:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;(sample 1 class) (space) (sample 2 class) (space) ... (sample N class)&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;For example:&lt;span style=&quot;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;&quot;&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;0 0 0 ... 1&lt;/span&gt;&lt;/code&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_CLS_File_Format:_Continuous&quot;&gt;&lt;/a&gt;CLS File Format: Continuous&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CLS file format defines phenotype (class or template) labels and associates each sample in the expression data with a label. The CLS file format uses spaces or tabs to separate the fields.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CLS file format differs somewhat depending on whether you are defining categorical or continuous phenotypes. Continuous phenotypes are used for time series experiments or to find gene sets correlations with a gene of interest (gene neighbors). For continuous labels, the CLS file format is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: cls_numeric_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: cls_time_series_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_GMX_File_Format&quot;&gt;&lt;/a&gt;GMX File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The GMX file format is a tab delimited file format that describes gene sets. In the GMX format, each column represents a gene set; in the GMT format, each row represents a gene set. The GMX file format is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: gmx_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_GMT_File_Format&quot;&gt;&lt;/a&gt;Each gene set is described by a name, a description, and the genes in the gene set. GSEA uses the description field to determine what hyperlink to provide in the report for the gene set description: if the description is &amp;ldquo;na&amp;rdquo;, GSEA provides a link to the named gene set in MSigDB; if the description is a URL, GSEA provides a link to that URL.&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;GMT File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The GMT file format is a tab delimited file format that describes gene sets. In the GMT format, each row represents a gene set; in the GMX format, each column represents a gene set. The GMT file format is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: gmt_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_GRP_File_Format&quot;&gt;&lt;/a&gt;Each gene set is described by a name, a description, and the genes in the gene set. GSEA uses the description field to determine what hyperlink to provide in the report for the gene set description: if the description is &amp;ldquo;na&amp;rdquo;, GSEA provides a link to the named gene set in MSigDB; if the description is a URL, GSEA provides a link to that URL.&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;GRP File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The GRP files contain a single gene set in a simple newline-delimited text format. Typically, you use the GMT or GMX file formats to create gene sets, rather than using the GRP file format. The GRP file format is organized as follows:&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: grp_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_CHIP_File_Format&quot;&gt;&lt;/a&gt;CHIP File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CHIP file contains annotation about a microarray. It should list the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available). While this file is not used directly in the GSEA algorithm, it is used to annotate the output results and may also be used to collapse each probe set in the expression dataset to a single gene vector. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: chip_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_CSV_File_Format_(for Chip Files)&quot;&gt;&lt;/a&gt;CSV File Format (for Chip Files)&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The CSV file format is identical to the CHIP file, except that the values in each row are separated by commas rather than by tabs. This file format is primarily used for Affymetrix chips.&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_RNK_File_Format&quot;&gt;&lt;/a&gt;RNK File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The RNK file contains a single, rank ordered gene list (&lt;em&gt;not&lt;/em&gt; gene set) in a simple newline-delimited text format. It is used when you have a pre-ordered ranked list that you want to analyze with GSEA. For instance, you might have used your favorite tTest-like statistic to produce a ranked ordered gene list from your dataset which you now want to test for enrichment. &lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: rnk_format_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;span style=&quot;&quot;&gt;&lt;a name=&quot;_MDB_File_Format&quot;&gt;&lt;/a&gt;MDB File Format&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p style=&quot;margin-bottom: 12pt;&quot; class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;The MDB files contain an entire gene set database. Unlike the gmt/gmx files, the MDB files are designed to contain rich annotation about a gene set. They are xml formatted file based on the MSigDB Document Type Definition (DTD). Following is the MSigDB DTD and a sample MDB file based on that DTD.&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong&gt;MSigDB DTD:&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: msigdb_dtd_snapshot.png]]&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;o:p&gt;&amp;nbsp;&lt;/o:p&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;&lt;strong&gt;Example of an MSigDB xml formatted file:&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;span style=&quot;&quot;&gt;[[image: msigdb_xml_snapshot.png]]&lt;/span&gt;&lt;/p&gt;</div> Tue, 28 Mar 2006 17:09:26 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Data_formats Gsea enhancements https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1495 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1495 <p>18.103.13.107: </p> <hr /> <div>&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/27 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. From the Load Data page: load a gene set matrix, use Extract Gene Sets to create gene sets in memory, use Create Ranked List to create a ranked list from one of those gene sets. It tells me that it created the ranked list and gives me the following info messages, but I can't find the ranked list: it's not in the default output folder, the object cache list, or the drop-downs on the PreRanked GSEA page. &lt;br /&gt;&lt;br /&gt;1355 [INFO ] Starting: =&amp;gt; Extract GeneSets from the GeneMatrix&lt;br /&gt;1385 [INFO ] Successfully created a GeneSet from the Dataset s2_gene_set_database.diabetes.gmt into: 323 gene sets&lt;br /&gt;1425 [INFO ] Null widget - no window opened&lt;br /&gt;9346 [INFO ] Starting: =&amp;gt; Create a RankedList&lt;br /&gt;9366 [INFO ] Successfully created a RankedList from the GeneSet 41BBPATHWAY into: 34 members&lt;br /&gt;9366 [INFO ] Null widget - no window opened&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/24 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. Names generaed by GSEA were too long for Windows. My personal profile failed to load and I was logged in with a temporary. Had to zip (and delete) one of my GSEA report folders before I could log into Windows with my own profile. Put the zipped reports folder in dropbox/foraravind.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Found/requested 3/22 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt; &lt;/span&gt;&lt;/span&gt;But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Indeed, if you set chip once for a dataset, the program remembers this association during the current session.&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed (note: it was clumsy to place a desc text in the table as it could be very long. So, the 2 modes are: 1) na in the desc field of the gmx /gmt file -&amp;gt; auto links to msigdb. 2) a valid url i.e text that starts with http &amp;gt; links to the custom http ... site specified&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;This is a 'feature'. The object cache lists the programs memory&amp;nbsp; while the leading edge cache lists the file system - i.e all analysis ever done (which could be too large to load into memory).&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;6. Analysis History page still isn't showing up for me. &lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;9. On the Algorithms page of the Preferences window, delete the phrase &amp;quot;(they can also be changed in params)&amp;quot; -- only one of them can.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;10. Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; 11. On the GSEA analysis report:&amp;nbsp; Indent the phenotype permutation warning (or make it another bullet) so it looks more like part of the &amp;quot;Other&amp;quot; section. Also, remove the message at the&amp;nbsp; bottom: &amp;quot;# of genesets before size filtering: 3 and # of genesets after size filtering: 3&amp;quot; (that info is already in the &amp;quot;Gene set details&amp;quot; section of the report).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Fixed&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;12. Leading Edge Viewer looks good! Two things: (1) The bottom two viewers have zoom controlled by CTRL+[ and CTRL+], but I can't get the focus to the right-hand viewer. The CTRL sequence always zooms the left viewer.&amp;nbsp; (2) The viewers completely replace the old HTML report, which included the details of gene sets used (name, # of members, # of members in signal, tag%, list%, signal strength). That info seems useful and now lost? (The 2nd viewer (the set-to-set comparison) has a nice open spot for a &amp;quot;Display gene set details&amp;quot; button...)&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Josh is adding 2) and can help fix 1).&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;1&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer&lt;br /&gt;2. Added a preferences field for path to user home dir.&lt;br /&gt;3. made native the default space in gsea. Not sure if this is better??&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt; I prefer gene_symbol since that's what we recommend.&lt;/span&gt;&lt;br /&gt;4. default collection of gene sets available via ftp&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/17:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Add Command button to Leading Edge page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Cant do this easilly because of the way the command thing is setup.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;You said you could do this after all.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Leading edge from command line give me fatal errors:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases&amp;nbsp;&amp;nbsp;&amp;nbsp; at &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip&amp;nbsp;&amp;nbsp;&amp;nbsp; at&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 799&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo&amp;nbsp;&amp;nbsp;&amp;nbsp; at&lt;br /&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&lt;br /&gt;Must set -DGSEA=true flag&lt;br /&gt;So,&lt;br /&gt;&lt;br /&gt; &lt;pre&gt;java -Xmx ... -DGSEA=true xtools.....&lt;/pre&gt; &lt;br /&gt;&lt;br /&gt;3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; Find sets that contain this gene page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 153, 0);&quot;&gt;Joshs reworked impl will replace this and the export option should be added to it&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On Run GSEA, change parameter name from &amp;quot;Analyze in the feature space&amp;quot; to &amp;quot;Gene/probe identifier format&amp;quot;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Lets talk. &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Forgot to bring this up in our last chat.&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 102, 0);&quot;&gt;What about using &amp;quot;Collapse dataset&amp;quot; as the name, where values are True (use 'chip' to collapse dataset to gene symbols) and False (blah blah).&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;5. Remove Downloads&amp;gt;Download Gene Sets (no longer needed now that we have MSigDB page).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;6. Change first two Help items to &amp;quot;GSEA web site&amp;quot; and &amp;quot;GSEA documentation&amp;quot;. First points to home page of web site and&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; second points to the doc page of the web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Bugs found 3/15/2006 include:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Generate a report, go to &amp;quot;Other&amp;quot; section, look at parameters. Error, file cannot be found.&lt;br /&gt;&lt;br /&gt;Fixed.&lt;br /&gt;&lt;br /&gt;2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.&lt;br /&gt;&lt;br /&gt;Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)&lt;br /&gt;&lt;br /&gt;3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.&lt;br /&gt;&lt;br /&gt;Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.</div> Mon, 27 Mar 2006 15:13:53 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_enhancements Gsea enhancements https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1426 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1426 <p>18.103.13.107: </p> <hr /> <div>As the software is almost perfect, there are few bugs and little need for enhancements.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/22 (with installed Gsea2):&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt; &lt;/span&gt;&lt;/span&gt;But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.&lt;br /&gt;&lt;br /&gt;2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)&lt;br /&gt;&lt;br /&gt;3. On Leading Edget report, when I click select reports from application cache, I expected to get today's reports (the ones in the Object Cache list on the Load Data page). Instead, I get a list of all reports, neatly arranged by date, excluding todays. When I run reports, they appear in the Object Cache as I expect.&lt;br /&gt;&lt;br /&gt;4. Run GSEA using the new Gene Matrix from web site tab to select the C2 gene sets. Analysis fails due to duplicate gene sets.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;&lt;/span&gt;5. On the new error handling, when I click the red error in the processes box, it should automatically open the console viewer and show me the error. It took me a litle bit to realize that I had to Click for details... to open the console and then click Error to see the error.&lt;br /&gt;&lt;br /&gt;6. Analysis History page still isn't showing up for me. &lt;br /&gt;&lt;br /&gt;7. On MSigDB page, when I click export, I'm expecting to export what I have displayed in the table on the MSigDB page. When I selected All Items, I thought that meant all items displayed in the table; it seems mean all items in the MSigDB? (thanks for going back to one button)&lt;br /&gt;&lt;br /&gt;8. RunGSEA form, the normalization parameter, you were going to delete the varmean option (or at least change the current name VarMeanPosNegSeparate back to varmean).&lt;br /&gt;&lt;br /&gt;9. On the Algorithms page of the Preferences window, delete the phrase &amp;quot;(they can also be changed in params)&amp;quot; -- only one of them can.&lt;br /&gt;&lt;br /&gt;10. Run GSEA, add a phenotypes file, create phenotypes on the fly (works fine), click the Show Phenotypes from all Sources. Should show labels from both the file you added and the one you just created, but now shows only one at a time. (This seems to have broken in the 3/21 build; I'm pretty sure it was working in the 3/20 build).&lt;br /&gt;&lt;br /&gt; 11. On the GSEA analysis report:&amp;nbsp; Indent the phenotype permutation warning (or make it another bullet) so it looks more like part of the &amp;quot;Other&amp;quot; section. Also, remove the message at the&amp;nbsp; bottom: &amp;quot;# of genesets before size filtering: 3 and # of genesets after size filtering: 3&amp;quot; (that info is already in the &amp;quot;Gene set details&amp;quot; section of the report).&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;1&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Leading edge interactive viewer&lt;br /&gt;2. Added a preferences field for path to user home dir.&lt;br /&gt;3. made native the default space in gsea. Not sure if this is better??&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt; I prefer gene_symbol since that's what we recommend.&lt;/span&gt;&lt;br /&gt;4. default collection of gene sets available via ftp&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/17:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Add Command button to Leading Edge page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Cant do this easilly because of the way the command thing is setup.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;You said you could do this after all.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Leading edge from command line give me fatal errors:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases&amp;nbsp;&amp;nbsp;&amp;nbsp; at &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip&amp;nbsp;&amp;nbsp;&amp;nbsp; at&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 799&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo&amp;nbsp;&amp;nbsp;&amp;nbsp; at&lt;br /&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&lt;br /&gt;Must set -DGSEA=true flag&lt;br /&gt;So,&lt;br /&gt;&lt;br /&gt; &lt;pre&gt;java -Xmx ... -DGSEA=true xtools.....&lt;/pre&gt; &lt;br /&gt;&lt;br /&gt;3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; Find sets that contain this gene page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 153, 0);&quot;&gt;Joshs reworked impl will replace this and the export option should be added to it&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On Run GSEA, change parameter name from &amp;quot;Analyze in the feature space&amp;quot; to &amp;quot;Gene/probe identifier format&amp;quot;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Lets talk. &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Forgot to bring this up in our last chat.&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;5. Remove Downloads&amp;gt;Download Gene Sets (no longer needed now that we have MSigDB page).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;6. Change first two Help items to &amp;quot;GSEA web site&amp;quot; and &amp;quot;GSEA documentation&amp;quot;. First points to home page of web site and&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; second points to the doc page of the web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Bugs found 3/15/2006 include:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;/span&gt;1. Generate a report, go to &amp;quot;Other&amp;quot; section, look at parameters. Error, file cannot be found.&lt;br /&gt;&lt;br /&gt;Fixed.&lt;br /&gt;&lt;br /&gt;2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.&lt;br /&gt;&lt;br /&gt;Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)&lt;br /&gt;&lt;br /&gt;3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.&lt;br /&gt;&lt;br /&gt;Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.</div> Wed, 22 Mar 2006 14:45:30 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_enhancements Gsea enhancements https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1416 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gsea_enhancements&diff=1416 <p>18.103.13.107: </p> <hr /> <div>As the software is almost perfect, there are few bugs and little need for enhancements.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/22&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;1. I expected chip or no chip specified to determine whether gene symbols/titles showed up in gene set detail report. Ran GSEA with p53, native, no chip, and got no gene symbol as expected. Added chip and got gene symbol as expected.&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt; &lt;/span&gt;&lt;/span&gt;But, then removed chip and still got the gene symbols (as if they were stored in memory or something). Parameters on the report confirm that I did not have chip specified. All three reports (nochip, chip, and chip_nochip) are in dropbox/foraravind.&lt;br /&gt;&lt;br /&gt;2. Created my own gene set file, one gene set with text description and another with URL. Ran GSEA. The Enrichment Result report tries to link my gene sets to MSigDB rather than using my descriptions. (That report also on the dropbox/foraravind.)&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;&lt;span style=&quot;font-weight: bold;&quot; /&gt;&lt;br /&gt;&lt;br /&gt;Feature Additions for build 3/2&lt;/span&gt;1&lt;br /&gt;&lt;br /&gt;1. Leading edge interactive viewer&lt;br /&gt;2. Added a preferences field for path to user home dir.&lt;br /&gt;3. made native the default space in gsea. Not sure if this is better??&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt; I prefer gene_symbol since that's what we recommend.&lt;/span&gt;&lt;br /&gt;4. default collection of gene sets available via ftp&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Found/requested 3/17:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;1. Add Command button to Leading Edge page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Cant do this easilly because of the way the command thing is setup.&lt;br /&gt;&lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;You said you could do this after all.&lt;/span&gt;&lt;br /&gt;&lt;/span&gt;&lt;br /&gt;2. Leading edge from command line give me fatal errors:&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\databases&amp;nbsp;&amp;nbsp;&amp;nbsp; at &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 719&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\chip2chip&amp;nbsp;&amp;nbsp;&amp;nbsp; at&amp;nbsp;&amp;nbsp; &lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; 799&amp;nbsp; [FATAL] Could not make dir: C:\Documents and Settings\hkuehn\.xtools_home\reports_cache_foo&amp;nbsp;&amp;nbsp;&amp;nbsp; at&lt;br /&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp;&amp;nbsp; edu.mit.broad.xbench.core.api.VdbManagerImpl._mkdir(VdbManagerImpl.java:89)&lt;br /&gt;&lt;br /&gt;Must set -DGSEA=true flag&lt;br /&gt;So,&lt;br /&gt;&lt;br /&gt; &lt;pre&gt;java -Xmx ... -DGSEA=true xtools.....&lt;/pre&gt; &lt;br /&gt;&lt;br /&gt;3. MSigDB page, the Find sets that Overlap search gives page with no Export button; make that page more like the&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; Find sets that contain this gene page.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 153, 0);&quot;&gt;Joshs reworked impl will replace this and the export option should be added to it&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;4. On Run GSEA, change parameter name from &amp;quot;Analyze in the feature space&amp;quot; to &amp;quot;Gene/probe identifier format&amp;quot;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(255, 0, 0);&quot;&gt;Lets talk. &lt;span style=&quot;color: rgb(0, 0, 255);&quot;&gt;Forgot to bring this up in our last chat.&lt;/span&gt;&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;5. Remove Downloads&amp;gt;Download Gene Sets (no longer needed now that we have MSigDB page).&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;6. Change first two Help items to &amp;quot;GSEA web site&amp;quot; and &amp;quot;GSEA documentation&amp;quot;. First points to home page of web site and&lt;br /&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; second points to the doc page of the web site.&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;color: rgb(51, 153, 102);&quot;&gt;Done&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;&lt;span style=&quot;font-weight: bold;&quot;&gt;Bugs found 3/15/2006 include:&lt;/span&gt;&lt;br /&gt;&lt;br /&gt;1. Generate a report, go to &amp;quot;Other&amp;quot; section, look at parameters. Error, file cannot be found.&lt;br /&gt;&lt;br /&gt;Fixed.&lt;br /&gt;&lt;br /&gt;2. Started a pretty long analysis, killed it. It took a few minutes versus a few seconds. If that's expected, perhaps change message to say may take a few minutes.&lt;br /&gt;&lt;br /&gt;Whats a long analysis? (for leading edge clustering more than a handful of sets, say 20, is likely pointless)&lt;br /&gt;&lt;br /&gt;3. Leading edge report brings up the gct files in a text editor rather than Excel; can't really read them in a text editor.&lt;br /&gt;&lt;br /&gt;Opening gct files now works like this: First check prefs to see if excel (or the other programs) exist at location indicated in the prefs. If so, use it. Otherwise issue a generic open file command in windows that will open up the file in whatever editor has been registered by windows for that file type. On the mac, the later mode is always done. On unix i dont know what will happen.</div> Wed, 22 Mar 2006 13:48:55 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Gsea_enhancements Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1403 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1403 <p>18.103.13.107: </p> <hr /> <div>The GSEA User Guide is provided in HTML, Word and PDF formats:&lt;br /&gt;&lt;br /&gt;[http://www.broad.mit.edu/personal/hkuehn/GSEADoc/GSEAUserGuide.htm GSEAUserGuide.htm]&lt;br /&gt;[http://www.broad.mit.edu/personal/hkuehn/GSEADoc/GSEAUserGuide.doc GSEAUserGuide.doc]&lt;br /&gt;[http://www.broad.mit.edu/personal/hkuehn/GSEADoc/GSEAUserGuide.pdf GSEAUserGuide.pdf]&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; This is a test of the Word-toWiki conversion. The text on this page is the documentation template; that is, various formats from the documentation.<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331825&quot;&gt;Heading 1&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot; style=&quot;&quot;&gt;Format for body text: &lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot; style=&quot;&quot;&gt;Format for headings (examples of each follow):&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 1&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 3&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331826&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Installing_GenePattern&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Heading 2&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt; for body text. Body text When you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for either local or distributed configurations.&lt;/p&gt;<br /> &lt;h3&gt;&lt;a name=&quot;_Toc127331827&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Starting_the_GenePattern_Java Clien&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Exiting_from_GenePattern&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Heading 3&lt;/span&gt;&lt;/h3&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt; for body text. &lt;/p&gt;<br /> &lt;h4&gt;Heading 4&lt;/h4&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Rarely used, but should be supported.&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331828&quot;&gt;Bulleted and Numbered Lists&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;For bulleted lists, use&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;List Continue&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListBullet2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListBullet2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 80px;&quot; class=&quot;MsoListContinue2&quot;&gt;List Continue 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;For numbered lists, use:&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListContinue&quot;&gt;List Continue&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 80px;&quot; class=&quot;MsoListContinue2&quot;&gt;List Continue 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;3.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;4.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Numbered and bulleted lists can be mixed:&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot; style=&quot;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number: hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListBullet2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 80px;&quot; class=&quot;MsoListContinue2&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListBullet2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 80px;&quot; class=&quot;MsoListContinue2&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot; style=&quot;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 80px;&quot; class=&quot;MsoListContinue2&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot; style=&quot;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;3.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331829&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Getting_Help&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Text Formats&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Within paragraph text, we use a number of character formats:&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Hyperlinks: &lt;span class=&quot;MsoHyperlink&quot;&gt;hyperlink&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;!--[endif]--&gt;Code and file names: &lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;em&gt;&lt;span style=&quot;font-style: normal;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/em&gt;&lt;!--[endif]--&gt;For GUI items, like menus and buttons: &lt;em&gt;br_GUI&lt;o:p&gt;&lt;/o:p&gt;&lt;/em&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;For menus, we use angle brackets, which need to be preserved: &lt;em&gt;File&amp;gt;Open&lt;/em&gt;. &lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;var&gt;&lt;span style=&quot;font-style: normal;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/var&gt;&lt;!--[endif]--&gt;For variables (this looks the same as GUI, but might in the future): &lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;For various reasons, most formats can be bold. So bold needs to be preserved.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot;&gt;Normal formats: &lt;st1:city w:st=&quot;on&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;Normal&lt;/st1:place&gt;&lt;/st1:city&gt;, &lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code, &lt;/span&gt;&lt;/code&gt;&lt;em&gt;br_GUI, &lt;/em&gt;&lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot;&gt;Bold formats: &lt;st1:city w:st=&quot;on&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;strong style=&quot;&quot;&gt;Normal&lt;/strong&gt;&lt;/st1:place&gt;&lt;/st1:city&gt;&lt;strong style=&quot;&quot;&gt;, &lt;/strong&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code, &lt;/span&gt;&lt;/code&gt;&lt;em&gt;br_GUI, &lt;/em&gt;&lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331830&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Working_with_Projects&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Header and Footer&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;The headers and footers would normally come over to html, but just for completeness, those formats would be&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Header: &lt;span class=&quot;HeaderChar&quot;&gt;header text&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span class=&quot;FooterChar&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Footer: &lt;span class=&quot;FooterChar&quot;&gt;footer text&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331831&quot;&gt;Tables and Graphics&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Tables need to come over cleanly. It&amp;rsquo;s hard to capture all formats, but here&amp;rsquo;s a basic table:&lt;/p&gt;<br /> &lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;1&quot; class=&quot;MsoTableGrid&quot; style=&quot;border: medium none ; border-collapse: collapse;&quot;&gt;<br /> &lt;tbody&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border: 1pt solid windowtext; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Column Header&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Column Header&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Bulleted stuff, stuff, stuff. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot; style=&quot;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Numbered stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/tbody&gt;<br /> &lt;/table&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;o:p&gt;&amp;nbsp;&lt;/o:p&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;In Word, graphics are linked in files. They also need to come over:&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shapetype id=&quot;_x0000_t75&quot; coordsize=&quot;21600,21600&quot;<br /> o:spt=&quot;75&quot; o:preferrelative=&quot;t&quot; path=&quot;m@4@5l@4@11@9@11@9@5xe&quot; filled=&quot;f&quot;<br /> stroked=&quot;f&quot;&gt;<br /> &lt;v:stroke joinstyle=&quot;miter&quot; /&gt;<br /> &lt;v:formulas&gt;<br /> &lt;v:f eqn=&quot;if lineDrawn pixelLineWidth 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @0 1 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum 0 0 @1&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @2 1 2&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @3 21600 pixelWidth&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @3 21600 pixelHeight&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @0 0 1&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @6 1 2&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @7 21600 pixelWidth&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @8 21600 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @7 21600 pixelHeight&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @10 21600 0&quot; /&gt;<br /> &lt;/v:formulas&gt;<br /> &lt;v:path o:extrusionok=&quot;f&quot; gradientshapeok=&quot;t&quot; o:connecttype=&quot;rect&quot; /&gt;<br /> &lt;o:lock v:ext=&quot;edit&quot; aspectratio=&quot;t&quot; /&gt;<br /> &lt;/v:shapetype&gt;&lt;v:shape id=&quot;_x0000_i1025&quot; type=&quot;#_x0000_t75&quot; style='width:14.25pt;<br /> height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-res.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;In rare cases, graphics appear in tables. Here&amp;rsquo;s an example:&lt;/p&gt;<br /> &lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;1&quot; class=&quot;MsoTableGrid&quot; style=&quot;border: medium none ; margin-left: 5.4pt; border-collapse: collapse;&quot;&gt;<br /> &lt;tbody&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border: 1pt solid windowtext; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1026&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:14.25pt;height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-res.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (res) &lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1027&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:14.25pt;height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-gct.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (gct)&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1028&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:13.5pt;height:13.5pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-pcl.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (pcl)&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/tbody&gt;<br /> &lt;/table&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331832&quot;&gt;Content&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;The introduction to each section that has subsections, should provide hyperlinks to the subsections. &lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;This section describes how to work with project directories in GenePattern:&lt;br /&gt;&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;[[#Opening_a_Project_Directory]]&lt;/li&gt;<br /> &lt;li&gt;[[#Opening_a_Project_Directory]]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> For more information, see the [http://wwwdev.broad.mit.edu/gsea/ GSEA web site].<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt; &lt;a href=&quot;#_Opening_a_Project_Directory&quot;&gt;&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&lt;span style=&quot;text-decoration: underline;&quot;&gt;&lt;/span&gt;&lt;/span&gt;&lt;/a&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331833&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Opening_a_Project_Directory&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Projects_Pane&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Projects Pane&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331834&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Opening_a_Project_Directory_1&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Opening a Project Directory&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;</div> Tue, 21 Mar 2006 21:27:09 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1400 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1400 <p>18.103.13.107: </p> <hr /> <div>The GSEA User Guide is provided in two formats, Word and PDF:&lt;br /&gt;&lt;br /&gt;[http://www.broad.mit.edu/personal/hkuehn/GSEADoc/GSEAUserGuide.doc GSEAUserGuide.doc]&lt;br /&gt;[http://www.broad.mit.edu/personal/hkuehn/GSEADoc/GSEAUserGuide.pdf GSEAUserGuide.pdf]&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt; This is a test of the Word-toWiki conversion. The text on this page is the documentation template; that is, various formats from the documentation.<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331825&quot;&gt;Heading 1&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;Format for body text: &lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt;&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoNormal&quot;&gt;Format for headings (examples of each follow):&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 1&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Heading 3&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331826&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Installing_GenePattern&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Heading 2&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt; for body text. Body text When you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for either local or distributed configurations.&lt;/p&gt;<br /> &lt;h3&gt;&lt;a name=&quot;_Toc127331827&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Starting_the_GenePattern_Java Clien&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Exiting_from_GenePattern&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Heading 3&lt;/span&gt;&lt;/h3&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;st1:city w:st=&quot;on&quot;&gt;Normal&lt;/st1:city&gt;&lt;/st1:place&gt; for body text. &lt;/p&gt;<br /> &lt;h4&gt;Heading 4&lt;/h4&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Rarely used, but should be supported.&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331828&quot;&gt;Bulleted and Numbered Lists&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;For bulleted lists, use&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot; style=&quot;margin-left: 40px;&quot;&gt;List Continue&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue2&quot; style=&quot;margin-left: 80px;&quot;&gt;List Continue 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;For numbered lists, use:&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot; style=&quot;margin-left: 40px;&quot;&gt;List Continue&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue2&quot; style=&quot;margin-left: 80px;&quot;&gt;List Continue 2hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;3.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;4.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Numbered and bulleted lists can be mixed:&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number: hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2 hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue2&quot; style=&quot;margin-left: 80px;&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;▪&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List Bullet 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue2&quot; style=&quot;margin-left: 80px;&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;p style=&quot;margin-left: 40px;&quot; class=&quot;MsoListNumber2&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber2&quot; style=&quot;margin-left: 40px;&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number 2&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue2&quot; style=&quot;margin-left: 80px;&quot;&gt;List Continue 2&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;3.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;List number.&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331829&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Getting_Help&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Text Formats&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Within paragraph text, we use a number of character formats:&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Hyperlinks: &lt;span class=&quot;MsoHyperlink&quot;&gt;hyperlink&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/code&gt;&lt;!--[endif]--&gt;Code and file names: &lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/code&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;em&gt;&lt;span style=&quot;font-style: normal;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/em&gt;&lt;!--[endif]--&gt;For GUI items, like menus and buttons: &lt;em&gt;br_GUI&lt;o:p&gt;&lt;/o:p&gt;&lt;/em&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;For menus, we use angle brackets, which need to be preserved: &lt;em&gt;File&amp;gt;Open&lt;/em&gt;. &lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;var&gt;&lt;span style=&quot;font-style: normal;&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/var&gt;&lt;!--[endif]--&gt;For variables (this looks the same as GUI, but might in the future): &lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;For various reasons, most formats can be bold. So bold needs to be preserved.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot;&gt;Normal formats: &lt;st1:city w:st=&quot;on&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;Normal&lt;/st1:place&gt;&lt;/st1:city&gt;, &lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code, &lt;/span&gt;&lt;/code&gt;&lt;em&gt;br_GUI, &lt;/em&gt;&lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListContinue&quot;&gt;Bold formats: &lt;st1:city w:st=&quot;on&quot;&gt;&lt;st1:place w:st=&quot;on&quot;&gt;&lt;strong style=&quot;&quot;&gt;Normal&lt;/strong&gt;&lt;/st1:place&gt;&lt;/st1:city&gt;&lt;strong style=&quot;&quot;&gt;, &lt;/strong&gt;&lt;code&gt;&lt;span style=&quot;font-size: 10pt;&quot;&gt;br_code, &lt;/span&gt;&lt;/code&gt;&lt;em&gt;br_GUI, &lt;/em&gt;&lt;var&gt;br_variable&lt;o:p&gt;&lt;/o:p&gt;&lt;/var&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331830&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Working_with_Projects&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Header and Footer&lt;/span&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;The headers and footers would normally come over to html, but just for completeness, those formats would be&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Header: &lt;span class=&quot;HeaderChar&quot;&gt;header text&lt;/span&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span class=&quot;FooterChar&quot;&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Footer: &lt;span class=&quot;FooterChar&quot;&gt;footer text&lt;o:p&gt;&lt;/o:p&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331831&quot;&gt;Tables and Graphics&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Tables need to come over cleanly. It&amp;rsquo;s hard to capture all formats, but here&amp;rsquo;s a basic table:&lt;/p&gt;<br /> &lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;1&quot; style=&quot;border: medium none ; border-collapse: collapse;&quot; class=&quot;MsoTableGrid&quot;&gt;<br /> &lt;tbody&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border: 1pt solid windowtext; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Column Header&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Column Header&lt;o:p&gt;&lt;/o:p&gt;&lt;/strong&gt;&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Bulleted stuff, stuff, stuff. hen you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for&lt;/p&gt;<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;●&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;p style=&quot;&quot; class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;1.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Numbered stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;p class=&quot;MsoListNumber&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt;2.&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;!--[endif]--&gt;Stuff, stuff, stuff.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;319&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/tbody&gt;<br /> &lt;/table&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;o:p&gt;&amp;nbsp;&lt;/o:p&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;In Word, graphics are linked in files. They also need to come over:&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shapetype id=&quot;_x0000_t75&quot; coordsize=&quot;21600,21600&quot;<br /> o:spt=&quot;75&quot; o:preferrelative=&quot;t&quot; path=&quot;m@4@5l@4@11@9@11@9@5xe&quot; filled=&quot;f&quot;<br /> stroked=&quot;f&quot;&gt;<br /> &lt;v:stroke joinstyle=&quot;miter&quot; /&gt;<br /> &lt;v:formulas&gt;<br /> &lt;v:f eqn=&quot;if lineDrawn pixelLineWidth 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @0 1 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum 0 0 @1&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @2 1 2&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @3 21600 pixelWidth&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @3 21600 pixelHeight&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @0 0 1&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @6 1 2&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @7 21600 pixelWidth&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @8 21600 0&quot; /&gt;<br /> &lt;v:f eqn=&quot;prod @7 21600 pixelHeight&quot; /&gt;<br /> &lt;v:f eqn=&quot;sum @10 21600 0&quot; /&gt;<br /> &lt;/v:formulas&gt;<br /> &lt;v:path o:extrusionok=&quot;f&quot; gradientshapeok=&quot;t&quot; o:connecttype=&quot;rect&quot; /&gt;<br /> &lt;o:lock v:ext=&quot;edit&quot; aspectratio=&quot;t&quot; /&gt;<br /> &lt;/v:shapetype&gt;&lt;v:shape id=&quot;_x0000_i1025&quot; type=&quot;#_x0000_t75&quot; style='width:14.25pt;<br /> height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-res.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;In rare cases, graphics appear in tables. Here&amp;rsquo;s an example:&lt;/p&gt;<br /> &lt;table cellspacing=&quot;0&quot; cellpadding=&quot;0&quot; border=&quot;1&quot; style=&quot;border: medium none ; margin-left: 5.4pt; border-collapse: collapse;&quot; class=&quot;MsoTableGrid&quot;&gt;<br /> &lt;tbody&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border: 1pt solid windowtext; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1026&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:14.25pt;height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-res.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (res) &lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1027&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:14.25pt;height:14.25pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-gct.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (gct)&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr style=&quot;&quot;&gt;<br /> &lt;td width=&quot;72&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;&lt;!--[if gte vml 1]&gt;&lt;v:shape id=&quot;_x0000_i1028&quot; type=&quot;#_x0000_t75&quot;<br /> style='width:13.5pt;height:13.5pt'&gt;<br /> &lt;v:imagedata src=&quot;images/icon-file-pcl.gif&quot; /&gt;<br /> &lt;/v:shape&gt;&lt;![endif]--&gt;&lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;[[Image: icon-file-gct.gif]]&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;td width=&quot;559&quot; valign=&quot;top&quot; style=&quot;border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;&quot;&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Expression dataset (pcl)&lt;/p&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/tbody&gt;<br /> &lt;/table&gt;<br /> &lt;h1&gt;&lt;a name=&quot;_Toc127331832&quot;&gt;Content&lt;/a&gt;&lt;/h1&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;The introduction to each section that has subsections, should provide hyperlinks to the subsections. &lt;/p&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;This section describes how to work with project directories in GenePattern:&lt;br /&gt;&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;[[#Opening_a_Project_Directory]]&lt;/li&gt;<br /> &lt;li&gt;[[#Opening_a_Project_Directory]]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> For more information, see the [http://wwwdev.broad.mit.edu/gsea/ GSEA web site].<br /> &lt;p class=&quot;MsoListBullet&quot;&gt;&lt;!--[if !supportLists]--&gt;&lt;span style=&quot;&quot;&gt; &lt;a href=&quot;#_Opening_a_Project_Directory&quot;&gt;&lt;span style=&quot;font-family: &amp;quot;Times New Roman&amp;quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;&quot;&gt;&lt;span style=&quot;text-decoration: underline;&quot;&gt;&lt;/span&gt;&lt;/span&gt;&lt;/a&gt;&lt;/span&gt;&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331833&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Opening_a_Project_Directory&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Projects_Pane&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Projects Pane&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;<br /> &lt;h2&gt;&lt;a name=&quot;_Toc127331834&quot;&gt;&lt;/a&gt;&lt;a name=&quot;_Opening_a_Project_Directory_1&quot;&gt;&lt;/a&gt;&lt;span style=&quot;&quot;&gt;Opening a Project Directory&lt;/span&gt;&lt;/h2&gt;<br /> &lt;p class=&quot;MsoNormal&quot;&gt;Blah, blah, blah.&lt;/p&gt;</div> Tue, 21 Mar 2006 21:21:26 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1297 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=1297 <p>18.103.13.107: </p> <hr /> <div>Wiki software successfully installed.<br /> <br /> Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]<br /> and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.<br /> <br /> <br /> This is a test<br /> '''Hello World'''<br /> <br /> <br /> [[This is another test.]]<br /> <br /> This is yet another test.<br /> <br /> <br /> more testting:<br /> [[MediaWiki:Sidebar]]</div> Tue, 14 Mar 2006 21:59:24 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Talk:Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1284 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1284 <p>18.103.13.107: </p> <hr /> <div>[[Documentation test]]</div> Fri, 10 Feb 2006 15:59:54 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Talk:Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1283 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1283 <p>18.103.13.107: </p> <hr /> <div></div> Fri, 10 Feb 2006 15:51:09 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page Talk:Main Page https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1282 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Talk:Main_Page&diff=1282 <p>18.103.13.107: </p> <hr /> <div><br /> Heidi testing wiki for documentation.</div> Fri, 10 Feb 2006 15:50:27 GMT 18.103.13.107 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:Main_Page