https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1006&feed=atom&action=history 1006 - Revision history 2024-03-29T11:17:26Z Revision history for this page on the wiki MediaWiki 1.34.4 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1006&diff=2542&oldid=prev Hkuehn at 17:01, 12 January 2007 2007-01-12T17:01:20Z <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 17:01, 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="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>The metric that you selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter (Signal2Noise or tTest) requires that you have at least three samples for each phenotype. You have too few samples for at least one of the phenotypes selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Phenotype labels&lt;/span&gt; parameter .&lt;br /&gt;&lt;br /&gt;To analyze a categorical phenotype that has fewer than three samples, use one of the following ranking metrics:&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>The metric that you selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter (Signal2Noise or tTest) requires that you have at least three samples for each phenotype. You have too few samples for at least one of the phenotypes selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Phenotype labels&lt;/span&gt; parameter .&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;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>To analyze a categorical phenotype that has fewer than three samples, use one of the following ranking metrics:&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;ul&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;ul&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;li&gt;Ratio_of_classes&lt;/li&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;li&gt;Ratio_of_classes&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td> <td colspan="2" class="diff-lineno">Line 7:</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;li&gt;Diff_of_classes&lt;/li&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;li&gt;Diff_of_classes&lt;/li&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;/ul&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;/ul&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;br /&gt;For information about the metrics, see the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter on the [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>Run_GSEA_Page Run GSEA Page] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&gt;For information about phenotypes, see [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>Phenotypes Phenotype Labels] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide. &lt;/em&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;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>For information about the metrics, see the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter on the [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>Run_GSEA_Page Run GSEA Page] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&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>For information about phenotypes, see [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>Phenotypes Phenotype Labels] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide. &lt;/em&gt;</div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1006&diff=2127&oldid=prev Hkuehn at 15:46, 15 December 2006 2006-12-15T15:46:34Z <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 15:46, 15 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>The metric that you selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter (Signal2Noise or tTest) requires that you have at least <del class="diffchange diffchange-inline">two </del>samples for each phenotype<del class="diffchange diffchange-inline">; however, you </del>have <del class="diffchange diffchange-inline">only one sample </del>for one of the phenotypes selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Phenotype labels&lt;/span&gt; parameter .&lt;br /&gt;&lt;br /&gt;To analyze a categorical phenotype that has <del class="diffchange diffchange-inline">only one sample</del>, use one of the following ranking metrics:&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>The metric that you selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter (Signal2Noise or tTest) requires that you have at least <ins class="diffchange diffchange-inline">three </ins>samples for each phenotype<ins class="diffchange diffchange-inline">. You </ins>have <ins class="diffchange diffchange-inline">too few samples </ins>for <ins class="diffchange diffchange-inline">at least </ins>one of the phenotypes selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Phenotype labels&lt;/span&gt; parameter .&lt;br /&gt;&lt;br /&gt;To analyze a categorical phenotype that has <ins class="diffchange diffchange-inline">fewer than three samples</ins>, use one of the following ranking metrics:&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;ul&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;ul&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;li&gt;Ratio_of_classes&lt;/li&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;li&gt;Ratio_of_classes&lt;/li&gt;</div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1006&diff=2088&oldid=prev Hkuehn at 19:52, 19 September 2006 2006-09-19T19:52:58Z <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 19:52, 19 September 2006</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</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;li&gt;Diff_of_classes&lt;/li&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;li&gt;Diff_of_classes&lt;/li&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;/ul&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;/ul&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>For information about the metrics, see the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter on the [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Run_GSEA_Page Run GSEA Page] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&gt;For information about phenotypes, see [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Phenotypes Phenotype Labels] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide. &lt;/em<del class="diffchange diffchange-inline">&gt;&lt;br /</del>&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><ins class="diffchange diffchange-inline">&lt;br /&gt;</ins>For information about the metrics, see the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter on the [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Run_GSEA_Page Run GSEA Page] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&gt;For information about phenotypes, see [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Phenotypes Phenotype Labels] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide. &lt;/em&gt;</div></td></tr> </table> Hkuehn https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=1006&diff=2087&oldid=prev Hkuehn at 19:52, 19 September 2006 2006-09-19T19:52:41Z <p></p> <p><b>New page</b></p><div>The metric that you selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter (Signal2Noise or tTest) requires that you have at least two samples for each phenotype; however, you have only one sample for one of the phenotypes selected in the &lt;span style=&quot;font-style: italic;&quot;&gt;Phenotype labels&lt;/span&gt; parameter .&lt;br /&gt;&lt;br /&gt;To analyze a categorical phenotype that has only one sample, use one of the following ranking metrics:&lt;br /&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Ratio_of_classes&lt;/li&gt;<br /> &lt;li&gt;log2_Ratio_of_classes&lt;/li&gt;<br /> &lt;li&gt;Diff_of_classes&lt;/li&gt;<br /> &lt;/ul&gt;<br /> For information about the metrics, see the &lt;span style=&quot;font-style: italic;&quot;&gt;Metric for ranking genes &lt;/span&gt;parameter on the [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Run_GSEA_Page Run GSEA Page] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide&lt;/em&gt;.&lt;br /&gt;For information about phenotypes, see [http://wwwdev.broad.mit.edu/gsea/doc/GSEAUserGuide.htm#Phenotypes Phenotype Labels] in the &lt;em style=&quot;&quot;&gt;GSEA User Guide. &lt;/em&gt;&lt;br /&gt;</div> Hkuehn