https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&feed=atom&action=historyXtools.gsea.Gsea - Revision history2024-03-28T17:13:23ZRevision history for this page on the wikiMediaWiki 1.34.4https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1734&oldid=prevHkuehn at 20:53, 11 April 20062006-04-11T20:53:40Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1734&oldid=1430">Show changes</a>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1430&oldid=prevHkuehn at 19:19, 22 March 20062006-03-22T19:19:02Z<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><p class="MsoNormal">Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. </p></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><p class="MsoNormal">Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. </p></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><p class="MsoNormal"><strong style="">Expression dataset.</strong> Select an <a href="#_Expression_Datasets">expression dataset</a> from the drop-down list. If the dataset is not listed, you have not yet loaded it; see <a href="#_Loading_Data_1">Loading Data</a>.</p></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><p class="MsoNormal"><strong style="">Expression dataset.</strong> Select an <a href="#_Expression_Datasets">expression dataset</a> from the drop-down list. If the dataset is not listed, you have not yet loaded it; see <a href="#_Loading_Data_1">Loading Data</a>.</p></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><p class="MsoNormal"><strong style="">Phenotype labels.</strong> Click the ellipse (&hellip;) button to display the <del class="diffchange diffchange-inline">following </del>window, which allows you to select one or more <a href="#_Phenotype_Labels_1">phenotypes</a> 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"><a href="#_Select_One_or_More Phenotypes Windo"></del>[[Cls <del class="diffchange diffchange-inline">Select One or More Phenotypes Window</a></del>]].</p></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><p class="MsoNormal"><strong style="">Phenotype labels.</strong> Click the ellipse (&hellip;) button to display the <ins class="diffchange diffchange-inline"><a href="#_Select_One_or_More Phenotypes Windo">Select One or More Phenotypes</a> </ins>window, which allows you to select one or more <a href="#_Phenotype_Labels_1">phenotypes</a> 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]].</p></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><p class="MsoNormal"><strong style="">Gene sets database.</strong> Click the ellipse (&hellip;) button and select one or more <a href="#_Gene_Sets">gene sets</a>. For convenience, the gene set selection window lists different gene set formats in separate tabs: </p></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><p class="MsoNormal"><strong style="">Gene sets database.</strong> Click the ellipse (&hellip;) button and select one or more <a href="#_Gene_Sets">gene sets</a>. For convenience, the gene set selection window lists different gene set formats in separate tabs: </p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**</p></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><p class="MsoNormal"><strong style="">Metric for ranking genes.</strong> As described in the &lt;Gene Set Enrichment Analysis&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.</p></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><p class="MsoNormal"><strong style="">Metric for ranking genes.</strong> As described in the &lt;Gene Set Enrichment Analysis&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.</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:</p></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><p style="margin-left: 40px;<del class="diffchange diffchange-inline">" class="MsoListContinue2</del>">mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)</p></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><p <ins class="diffchange diffchange-inline">class="MsoListContinue2" </ins>style="margin-left: 40px;">mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)</p></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><p style="margin-left: 40px;<del class="diffchange diffchange-inline">" class="MsoListContinue2</del>">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 &ldquo;class marker.&rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select <em>Options&gt;Use median instead of mean for metrics</em>.)</p></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><p <ins class="diffchange diffchange-inline">class="MsoListContinue2" </ins>style="margin-left: 40px;">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 &ldquo;class marker.&rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select <em>Options&gt;Use median instead of mean for metrics</em>.)</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->tTest. **need explanations**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->tTest. **need explanations**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Cosine.</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Cosine.</p></div></td></tr>
</table>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1429&oldid=prevHkuehn at 19:16, 22 March 20062006-03-22T19:16:37Z<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><p class="MsoNormal">Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. </p></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><p class="MsoNormal">Required Fields lists parameters that are essential for the analysis. Enter values for these parameters before starting the analysis. </p></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><p class="MsoNormal"><strong style="">Expression dataset.</strong> Select an <a href="#_Expression_Datasets">expression dataset</a> from the drop-down list. If the dataset is not listed, you have not yet loaded it; see <a href="#_Loading_Data_1">Loading Data</a>.</p></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><p class="MsoNormal"><strong style="">Expression dataset.</strong> Select an <a href="#_Expression_Datasets">expression dataset</a> from the drop-down list. If the dataset is not listed, you have not yet loaded it; see <a href="#_Loading_Data_1">Loading Data</a>.</p></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><p class="MsoNormal"><strong style="">Phenotype labels.</strong> Click the ellipse (&hellip;) button to display the following window, which allows you to select one or more <a href="#_Phenotype_Labels_1">phenotypes</a> 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 <a href="#_Select_One_or_More Phenotypes Windo">Select One or More Phenotypes Window</a>.</p></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><p class="MsoNormal"><strong style="">Phenotype labels.</strong> Click the ellipse (&hellip;) button to display the following window, which allows you to select one or more <a href="#_Phenotype_Labels_1">phenotypes</a> 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 <a href="#_Select_One_or_More Phenotypes Windo"><ins class="diffchange diffchange-inline">[[Cls </ins>Select One or More Phenotypes Window</a><ins class="diffchange diffchange-inline">]]</ins>.</p></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><p class="MsoNormal"><strong style="">Gene sets database.</strong> Click the ellipse (&hellip;) button and select one or more <a href="#_Gene_Sets">gene sets</a>. For convenience, the gene set selection window lists different gene set formats in separate tabs: </p></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><p class="MsoNormal"><strong style="">Gene sets database.</strong> Click the ellipse (&hellip;) button and select one or more <a href="#_Gene_Sets">gene sets</a>. For convenience, the gene set selection window lists different gene set formats in separate tabs: </p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**</p></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><p class="MsoNormal"><strong style="">Metric for ranking genes.</strong> As described in the &lt;Gene Set Enrichment Analysis&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.</p></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><p class="MsoNormal"><strong style="">Metric for ranking genes.</strong> As described in the &lt;Gene Set Enrichment Analysis&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.</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Signal2Noise (default). The signal-to-noise ratio uses the following formula to determine differential gene expression with respect to two phenotypes:</p></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><p <del class="diffchange diffchange-inline">class="MsoListContinue2" </del>style="margin-left: 40px;">mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)</p></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><p style="margin-left: 40px;<ins class="diffchange diffchange-inline">" class="MsoListContinue2</ins>">mean in class_a - mean in class_b / (standard deviation class_a + standard deviation class_b)</p></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><p <del class="diffchange diffchange-inline">class="MsoListContinue2" </del>style="margin-left: 40px;">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 &ldquo;class marker.&rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select <em>Options&gt;Use median instead of mean for metrics</em>.)</p></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><p style="margin-left: 40px;<ins class="diffchange diffchange-inline">" class="MsoListContinue2</ins>">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 &ldquo;class marker.&rdquo; (To have GSEA use the median of class_a minus the median of class_b in this calculation, select <em>Options&gt;Use median instead of mean for metrics</em>.)</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->tTest. **need explanations**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->tTest. **need explanations**</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Cosine.</p></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><p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Cosine.</p></div></td></tr>
</table>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1428&oldid=prevHkuehn at 19:15, 22 March 20062006-03-22T19:15:18Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<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>
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<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"><p class="MsoNormal">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 <em>Run</em>. You can also run the analysis from the command line, as described in <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"><p class="MsoNormal">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 <em>Run</em>. You can also run the analysis from the command line, as described in <a </ins></div></td></tr>
</table>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1397&oldid=prevHkuehn at 21:10, 21 March 20062006-03-21T21:10:12Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1397&oldid=1395">Show changes</a>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1395&oldid=prevHkuehn at 20:58, 21 March 20062006-03-21T20:58:33Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1395&oldid=1394">Show changes</a>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1394&oldid=prevHkuehn at 20:55, 21 March 20062006-03-21T20:55:29Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1394&oldid=1392">Show changes</a>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1392&oldid=prevHkuehn at 20:48, 21 March 20062006-03-21T20:48:56Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1392&oldid=1390">Show changes</a>Hkuehnhttps://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1390&oldid=prevHkuehn at 20:42, 21 March 20062006-03-21T20:42:40Z<p></p>
<a href="https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Xtools.gsea.Gsea&diff=1390">Show changes</a>Hkuehn