1002 - Revision history https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&action=history Revision history for this page on the wiki en MediaWiki 1.34.4 Thu, 28 Mar 2024 18:23:20 GMT Acastanza: Revised for new parameter name https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=4443&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=4443&oldid=prev <p>Revised for new parameter name</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 19:55, 20 March 2021</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse <del class="diffchange diffchange-inline">dataset </del>to gene symbols&lt;/span&gt; parameter to <del class="diffchange diffchange-inline">True</del>, you must select one or more chip annotation files using the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse<ins class="diffchange diffchange-inline">/Remap </ins>to gene symbols&lt;/span&gt; parameter to <ins class="diffchange diffchange-inline">&quot;Collapse&quot; or &quot;Remap_only&quot;</ins>, you must select one or more chip annotation files using the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse <del class="diffchange diffchange-inline">dataset </del>to gene symbols&lt;/span&gt; parameter to <del class="diffchange diffchange-inline">True </del>tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do <del class="diffchange diffchange-inline">this</del>, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. The chip annotation file(s) supply that mapping information. For more information, see&amp;nbsp;  [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html?Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse<ins class="diffchange diffchange-inline">/Remap </ins>to gene symbols&lt;/span&gt; parameter to <ins class="diffchange diffchange-inline">&quot;Collapse&quot; </ins>tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol<ins class="diffchange diffchange-inline">. In contrast, &quot;Remap_only&quot; uses the information in the chip to perform simple, non-mathematical translations of gene identifiers from one format to another</ins>. To do <ins class="diffchange diffchange-inline">these operations</ins>, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. The chip annotation file(s) supply that mapping information. For more information, see&amp;nbsp;  [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html?Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&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&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&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse <del class="diffchange diffchange-inline">dataset </del>to gene symbols&lt;/span&gt; parameter to <del class="diffchange diffchange-inline">False</del>. In this case, GSEA does not <del class="diffchange diffchange-inline">collapse </del>your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is <del class="diffchange diffchange-inline">optional. If you specify it, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted</del>.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse<ins class="diffchange diffchange-inline">/Remap </ins>to gene symbols&lt;/span&gt; parameter to <ins class="diffchange diffchange-inline">&quot;No_Collapse&quot;</ins>. In this case, GSEA does not <ins class="diffchange diffchange-inline">perform any mapping operations on </ins>your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is <ins class="diffchange diffchange-inline">not used</ins>.&lt;br /&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&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&gt;</div></td></tr> </table> Sat, 20 Mar 2021 19:55:49 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 17:02, 12 January 2007 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=2543&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=2543&oldid=prev <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 17:02, 12 January 2007</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="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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select one or more chip annotation files using the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select one or more chip annotation files using the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. The chip annotation file(s) supply that mapping information. For more information, see&amp;nbsp;  <del class="diffchange diffchange-inline">&lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;</del>[http://<del class="diffchange diffchange-inline">wwwdev</del>.broad.mit.edu/gsea/doc/<del class="diffchange diffchange-inline">GSEAUserGuide</del>.<del class="diffchange diffchange-inline">htm#</del>Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. The chip annotation file(s) supply that mapping information. For more information, see&amp;nbsp;  [http://<ins class="diffchange diffchange-inline">www</ins>.broad.mit.edu/gsea/doc/<ins class="diffchange diffchange-inline">GSEAUserGuideFrame</ins>.<ins class="diffchange diffchange-inline">html?</ins>Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, GSEA does not collapse your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If you specify it, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&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&gt;</div></td></tr> <tr><td colspan="2"> </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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, GSEA does not collapse your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If you specify it, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;</div></td></tr> <tr><td colspan="2"> </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&gt;</div></td></tr> </table> Fri, 12 Jan 2007 17:02:50 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 19:12, 19 December 2006 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=2150&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=2150&oldid=prev <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 19:12, 19 December 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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select <del class="diffchange diffchange-inline">a </del>chip <del class="diffchange diffchange-inline">for </del>the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select <ins class="diffchange diffchange-inline">one or more </ins>chip <ins class="diffchange diffchange-inline">annotation files using </ins>the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. <del class="diffchange diffchange-inline">You </del>supply that mapping information <del class="diffchange diffchange-inline">by clicking the </del>.<del class="diffchange diffchange-inline">.. button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need</del>, <del class="diffchange diffchange-inline">you can download or create additional chip annotation files (</del>see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt; <del class="diffchange diffchange-inline">for more information)</del>.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. <ins class="diffchange diffchange-inline">The chip annotation file(s) </ins>supply that mapping information. <ins class="diffchange diffchange-inline">For more information</ins>, see<ins class="diffchange diffchange-inline">&amp;nbsp;  </ins>&lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, GSEA does not collapse your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If you specify it, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, GSEA does not collapse your dataset and the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If you specify it, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;&lt;/p&gt;</div></td></tr> </table> Tue, 19 Dec 2006 19:12:03 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 15:22, 4 April 2006 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1649&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1649&oldid=prev <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 15:22, 4 April 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="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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide &lt;/em&gt;for more information <del class="diffchange diffchange-inline">about downloading or creating additional chip annotation files</del>.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which gets identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, <ins class="diffchange diffchange-inline">you can download or create additional chip annotation files (</ins>see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt; for more information<ins class="diffchange diffchange-inline">)</ins>.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If <del class="diffchange diffchange-inline">specified</del>, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, <ins class="diffchange diffchange-inline">GSEA does not collapse your dataset and </ins>the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If <ins class="diffchange diffchange-inline">you specify it</ins>, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;&lt;/p&gt;</div></td></tr> </table> Tue, 04 Apr 2006 15:22:50 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 15:20, 4 April 2006 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1648&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1648&oldid=prev <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 15:20, 4 April 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="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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which <del class="diffchange diffchange-inline">get </del>identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide &lt;/em&gt;for more information about downloading or creating additional chip annotation files.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which <ins class="diffchange diffchange-inline">gets </ins>identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide &lt;/em&gt;for more information about downloading or creating additional chip annotation files.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If specified, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If specified, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;&lt;/p&gt;</div></td></tr> </table> Tue, 04 Apr 2006 15:20:20 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 15:19, 4 April 2006 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1647&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1647&oldid=prev <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 15:19, 4 April 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="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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.</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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which get identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;for more information about downloading or creating additional chip annotation files.&lt;br /&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&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which get identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span<ins class="diffchange diffchange-inline">&gt;[http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Chip_Annotations DNA Chip (Array) Annotations] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide &lt;/em</ins>&gt;for more information about downloading or creating additional chip annotation files.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If specified, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&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&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If specified, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;&lt;/p&gt;</div></td></tr> </table> Tue, 04 Apr 2006 15:19:31 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002 Hkuehn at 15:18, 4 April 2006 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1646&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1002&diff=1646&oldid=prev <p></p> <p><b>New page</b></p><div>When you set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True, you must select a chip for the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter.<br /> &lt;p&gt;Setting the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to True tells GSEA to collapse each probe set in the dataset to a single vector for the gene, which get identified by its HUGO gene symbol. To do this, GSEA needs to map the probes in the dataset to their matching HUGO gene symbols. You supply that mapping information by clicking the ... button next to the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter and selecting the chip used to generate your dataset. If you do not see the chip that you need, see &lt;span style=&quot;font-size: 12pt; font-family: &amp;quot;Times New Roman&amp;quot;;&quot;&gt;&lt;/span&gt;for more information about downloading or creating additional chip annotation files.&lt;br /&gt;&lt;/p&gt;<br /> &lt;p&gt;Alternatively, you can set the &lt;span style=&quot;font-style: italic;&quot;&gt;Collapse dataset to gene symbols&lt;/span&gt; parameter to False. In this case, the &lt;span style=&quot;font-style: italic;&quot;&gt;Chip platform(s)&lt;/span&gt; parameter is optional. If specified, the analysis results report includes links to the HUGO gene symbols; otherwise, the links are omitted.&lt;br /&gt;&lt;/p&gt;</div> Tue, 04 Apr 2006 15:18:10 GMT Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:1002