https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&feed=atom&action=history Xtools.gsea.Gsea - Revision history 2024-03-28T17:13:23Z Revision history for this page on the wiki MediaWiki 1.34.4 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1734&oldid=prev Hkuehn at 20:53, 11 April 2006 2006-04-11T20:53:40Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1734&amp;oldid=1430">Show changes</a> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1430&oldid=prev Hkuehn at 19:19, 22 March 2006 2006-03-22T19:19:02Z <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:19, 22 March 2006</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. &lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. &lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Expression dataset.&lt;/strong&gt; Select an &lt;a href=&quot;#_Expression_Datasets&quot;&gt;expression dataset&lt;/a&gt; from the drop-down list. If the dataset is not listed, you have not yet loaded it; see &lt;a href=&quot;#_Loading_Data_1&quot;&gt;Loading Data&lt;/a&gt;.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Expression dataset.&lt;/strong&gt; Select an &lt;a href=&quot;#_Expression_Datasets&quot;&gt;expression dataset&lt;/a&gt; from the drop-down list. If the dataset is not listed, you have not yet loaded it; see &lt;a href=&quot;#_Loading_Data_1&quot;&gt;Loading Data&lt;/a&gt;.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Phenotype labels.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button to display the <del class="diffchange diffchange-inline">following </del>window, which allows you to select one or more &lt;a href=&quot;#_Phenotype_Labels_1&quot;&gt;phenotypes&lt;/a&gt; to analyze. GSEA will analyze each phenotype separately, producing a single report that contains all of the analysis results. For more information about this window, see <del class="diffchange diffchange-inline">&lt;a href=&quot;#_Select_One_or_More Phenotypes Windo&quot;&gt;</del>[[Cls <del class="diffchange diffchange-inline">Select One or More Phenotypes Window&lt;/a&gt;</del>]].&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Phenotype labels.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button to display the <ins class="diffchange diffchange-inline">&lt;a href=&quot;#_Select_One_or_More Phenotypes Windo&quot;&gt;Select One or More Phenotypes&lt;/a&gt; </ins>window, which allows you to select one or more &lt;a href=&quot;#_Phenotype_Labels_1&quot;&gt;phenotypes&lt;/a&gt; to analyze. GSEA will analyze each phenotype separately, producing a single report that contains all of the analysis results. For more information about this window, see [[Cls]].&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Gene sets database.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button and select one or more &lt;a href=&quot;#_Gene_Sets&quot;&gt;gene sets&lt;/a&gt;. For convenience, the gene set selection window lists different gene set formats in separate tabs: &lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Gene sets database.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button and select one or more &lt;a href=&quot;#_Gene_Sets&quot;&gt;gene sets&lt;/a&gt;. For convenience, the gene set selection window lists different gene set formats in separate tabs: &lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**&lt;/p&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30" >Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Metric for ranking genes.&lt;/strong&gt; As described in the &amp;lt;Gene Set Enrichment Analysis&amp;gt; PNAS paper, GSEA first orders genes in a ranked list according to their differential expression. Use this parameter to select the metric that GSEA uses to rank the genes.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Metric for ranking genes.&lt;/strong&gt; As described in the &amp;lt;Gene Set Enrichment Analysis&amp;gt; PNAS paper, GSEA first orders genes in a ranked list according to their differential expression. Use this parameter to select the metric that GSEA uses to rank the genes.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p style=&quot;margin-left: 40px;<del class="diffchange diffchange-inline">&quot; class=&quot;MsoListContinue2</del>&quot;&gt;mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p <ins class="diffchange diffchange-inline">class=&quot;MsoListContinue2&quot; </ins>style=&quot;margin-left: 40px;&quot;&gt;mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p style=&quot;margin-left: 40px;<del class="diffchange diffchange-inline">&quot; class=&quot;MsoListContinue2</del>&quot;&gt;The larger the signal-to-noise ratio, the larger the differences of the means (scaled by the standard deviations); that is, the more distinct the gene expression is in each phenotype and the more the gene acts as a &amp;ldquo;class marker.&amp;rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select &lt;em&gt;Options&amp;gt;Use median instead of mean for metrics&lt;/em&gt;.)&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p <ins class="diffchange diffchange-inline">class=&quot;MsoListContinue2&quot; </ins>style=&quot;margin-left: 40px;&quot;&gt;The larger the signal-to-noise ratio, the larger the differences of the means (scaled by the standard deviations); that is, the more distinct the gene expression is in each phenotype and the more the gene acts as a &amp;ldquo;class marker.&amp;rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select &lt;em&gt;Options&amp;gt;Use median instead of mean for metrics&lt;/em&gt;.)&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;tTest. **need explanations**&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;tTest. **need explanations**&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Cosine.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Cosine.&lt;/p&gt;</div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1429&oldid=prev Hkuehn at 19:16, 22 March 2006 2006-03-22T19:16:37Z <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:16, 22 March 2006</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. &lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. &lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Expression dataset.&lt;/strong&gt; Select an &lt;a href=&quot;#_Expression_Datasets&quot;&gt;expression dataset&lt;/a&gt; from the drop-down list. If the dataset is not listed, you have not yet loaded it; see &lt;a href=&quot;#_Loading_Data_1&quot;&gt;Loading Data&lt;/a&gt;.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Expression dataset.&lt;/strong&gt; Select an &lt;a href=&quot;#_Expression_Datasets&quot;&gt;expression dataset&lt;/a&gt; from the drop-down list. If the dataset is not listed, you have not yet loaded it; see &lt;a href=&quot;#_Loading_Data_1&quot;&gt;Loading Data&lt;/a&gt;.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Phenotype labels.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button to display the following window, which allows you to select one or more &lt;a href=&quot;#_Phenotype_Labels_1&quot;&gt;phenotypes&lt;/a&gt; to analyze. GSEA will analyze each phenotype separately, producing a single report that contains all of the analysis results. For more information about this window, see &lt;a href=&quot;#_Select_One_or_More Phenotypes Windo&quot;&gt;Select One or More Phenotypes Window&lt;/a&gt;.&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Phenotype labels.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button to display the following window, which allows you to select one or more &lt;a href=&quot;#_Phenotype_Labels_1&quot;&gt;phenotypes&lt;/a&gt; to analyze. GSEA will analyze each phenotype separately, producing a single report that contains all of the analysis results. For more information about this window, see &lt;a href=&quot;#_Select_One_or_More Phenotypes Windo&quot;&gt;<ins class="diffchange diffchange-inline">[[Cls </ins>Select One or More Phenotypes Window&lt;/a&gt;<ins class="diffchange diffchange-inline">]]</ins>.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Gene sets database.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button and select one or more &lt;a href=&quot;#_Gene_Sets&quot;&gt;gene sets&lt;/a&gt;. For convenience, the gene set selection window lists different gene set formats in separate tabs: &lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Gene sets database.&lt;/strong&gt; Click the ellipse (&amp;hellip;) button and select one or more &lt;a href=&quot;#_Gene_Sets&quot;&gt;gene sets&lt;/a&gt;. For convenience, the gene set selection window lists different gene set formats in separate tabs: &lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**&lt;/p&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l30" >Line 30:</td> <td colspan="2" class="diff-lineno">Line 30:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Metric for ranking genes.&lt;/strong&gt; As described in the &amp;lt;Gene Set Enrichment Analysis&amp;gt; PNAS paper, GSEA first orders genes in a ranked list according to their differential expression. Use this parameter to select the metric that GSEA uses to rank the genes.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p class=&quot;MsoNormal&quot;&gt;&lt;strong style=&quot;&quot;&gt;Metric for ranking genes.&lt;/strong&gt; As described in the &amp;lt;Gene Set Enrichment Analysis&amp;gt; PNAS paper, GSEA first orders genes in a ranked list according to their differential expression. Use this parameter to select the metric that GSEA uses to rank the genes.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p <del class="diffchange diffchange-inline">class=&quot;MsoListContinue2&quot; </del>style=&quot;margin-left: 40px;&quot;&gt;mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p style=&quot;margin-left: 40px;<ins class="diffchange diffchange-inline">&quot; class=&quot;MsoListContinue2</ins>&quot;&gt;mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p <del class="diffchange diffchange-inline">class=&quot;MsoListContinue2&quot; </del>style=&quot;margin-left: 40px;&quot;&gt;The larger the signal-to-noise ratio, the larger the differences of the means (scaled by the standard deviations); that is, the more distinct the gene expression is in each phenotype and the more the gene acts as a &amp;ldquo;class marker.&amp;rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select &lt;em&gt;Options&amp;gt;Use median instead of mean for metrics&lt;/em&gt;.)&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p style=&quot;margin-left: 40px;<ins class="diffchange diffchange-inline">&quot; class=&quot;MsoListContinue2</ins>&quot;&gt;The larger the signal-to-noise ratio, the larger the differences of the means (scaled by the standard deviations); that is, the more distinct the gene expression is in each phenotype and the more the gene acts as a &amp;ldquo;class marker.&amp;rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select &lt;em&gt;Options&amp;gt;Use median instead of mean for metrics&lt;/em&gt;.)&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;tTest. **need explanations**&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;tTest. **need explanations**&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Cosine.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p 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;Cosine.&lt;/p&gt;</div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1428&oldid=prev Hkuehn at 19:15, 22 March 2006 2006-03-22T19:15:18Z <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:15, 22 March 2006</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;p class=&quot;MsoNormal&quot;&gt;Use the Run GSEA page to run the gene set enrichment analysis. Place your cursor on a parameter name to see a brief description of the parameter. To run the analysis, set the parameters and click &lt;em&gt;Run&lt;/em&gt;. You can also run the analysis from the command line, as described in &lt;a </del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">&lt;p class=&quot;MsoNormal&quot;&gt;Use the Run GSEA page to run the gene set enrichment analysis. Place your cursor on a parameter name to see a brief description of the parameter. To run the analysis, set the parameters and click &lt;em&gt;Run&lt;/em&gt;. You can also run the analysis from the command line, as described in &lt;a </ins></div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1397&oldid=prev Hkuehn at 21:10, 21 March 2006 2006-03-21T21:10:12Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1397&amp;oldid=1395">Show changes</a> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1395&oldid=prev Hkuehn at 20:58, 21 March 2006 2006-03-21T20:58:33Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1395&amp;oldid=1394">Show changes</a> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1394&oldid=prev Hkuehn at 20:55, 21 March 2006 2006-03-21T20:55:29Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1394&amp;oldid=1392">Show changes</a> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1392&oldid=prev Hkuehn at 20:48, 21 March 2006 2006-03-21T20:48:56Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1392&amp;oldid=1390">Show changes</a> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1390&oldid=prev Hkuehn at 20:42, 21 March 2006 2006-03-21T20:42:40Z <p></p> <a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&amp;diff=1390">Show changes</a> Hkuehn