FAQ - Revision history https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&action=history Revision history for this page on the wiki en MediaWiki 1.34.4 Thu, 28 Mar 2024 14:48:12 GMT Acastanza: Added commentary on non-finite errors in plotting https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4457&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4457&oldid=prev <p>Added commentary on non-finite errors in plotting</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 23:05, 12 November 2021</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l147" >Line 147:</td> <td colspan="2" class="diff-lineno">Line 147:</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;h4&gt;What does it mean for a gene set to have NES and nominal p-values of NaN (also shown as blanks)?&lt;/h4&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;h4&gt;What does it mean for a gene set to have NES and nominal p-values of NaN (also shown as blanks)?&lt;/h4&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;When adjusting for variation in gene set size, we normalize permuted ES(S, pi) and the observed ES(S) for a given S, separately rescaling the positive and negative scores by dividing by the mean of the ES(S, pi) to yield NES(S, pi) and NES(S). However, when the scores of the corresponding sign are absent, the mean ES(S, pi) = 0, and the division by zero will result in NaN values both for the NES(S, pi) and NES(S) as well as for the nominal p-values that follow from these calculations. The easiest way to overcome this issue would be to increase number of permutations. If this does not help, we recommend further exploring reasons for this bias. For example, it could be caused by a large difference in the number of samples of each phenotype class. For further details, please consult the GSEA PNAS 2005 paper, sections &quot;Multiple Hypothesis Testing&quot; in the &quot;Mathematical Description of Methods&quot; and the &quot;Supporting Text&quot; Appendix.&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;When adjusting for variation in gene set size, we normalize permuted ES(S, pi) and the observed ES(S) for a given S, separately rescaling the positive and negative scores by dividing by the mean of the ES(S, pi) to yield NES(S, pi) and NES(S). However, when the scores of the corresponding sign are absent, the mean ES(S, pi) = 0, and the division by zero will result in NaN values both for the NES(S, pi) and NES(S) as well as for the nominal p-values that follow from these calculations. The easiest way to overcome this issue would be to increase number of permutations. If this does not help, we recommend further exploring reasons for this bias. For example, it could be caused by a large difference in the number of samples of each phenotype class. For further details, please consult the GSEA PNAS 2005 paper, sections &quot;Multiple Hypothesis Testing&quot; in the &quot;Mathematical Description of Methods&quot; and the &quot;Supporting Text&quot; Appendix.&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><ins style="font-weight: bold; text-decoration: none;"></ins></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><ins style="font-weight: bold; text-decoration: none;">&lt;h4&gt;Why didn't my gene set display an enrichment plot even though it is in the top hits?&lt;/h4&gt;</ins></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><ins style="font-weight: bold; text-decoration: none;">&lt;p&gt;Sometimes when running GSEA with metrics other than signal-to-noise, or t-test, some plots may fail to render resulting in a Java error message being printed in red text in the place of the plot on the results page. This error is typically caused by GSEA encountering a divide-by-zero in the internal ranking metric computation, or an overflow where the result of the calculation between phenotypes returns an &quot;infinity&quot;. The presence of infinite values in the resulting internal ranked list can be confirmed by navigating to the GSEA results directory for the given run, opening the &quot;edb&quot; folder, and then inspecting the .rnk file in this directory for &quot;Inf&quot;, &quot;NaN&quot; or similar strings. It might be possible to resolve these issues by adding a small pseudocount to the dataset. It should be noted that any such selected value here is arbitrary and we do not advise the selection of any specific value, consult your local bioinformaticians for specific guidance. This error may also occur in GSEA Preranked mode, in which case these non-finite values would have been present in the supplied preranked list and should be resolved though the original quantification pipeline.&lt;/p&gt;</ins></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;"></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;"></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;h1&gt;MSigDB Gene Sets&lt;/h1&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;h1&gt;MSigDB Gene Sets&lt;/h1&gt;</div></td></tr> </table> Fri, 12 Nov 2021 23:05:14 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza at 16:30, 19 November 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4377&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4377&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 16:30, 19 November 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l37" >Line 37:</td> <td colspan="2" class="diff-lineno">Line 37:</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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;For detailed information on using RNA-seq data sets with GSEA, [[Using_RNA-seq_Datasets_with_GSEA|please see this help page.]]&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;For detailed information on using RNA-seq data sets with GSEA, [[Using_RNA-seq_Datasets_with_GSEA|please see this help page.]]&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; <del class="diffchange diffchange-inline">for </del>other data types, it is generally recommended to use GSEA-Preranked, where the features being analyzed have been quantitatively ranked in order of most (largest value) to least (smallest value) &quot;of interest&quot;&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;<ins class="diffchange diffchange-inline">For </ins>other data types, it is generally recommended to use GSEA-Preranked, where the features being analyzed have been quantitatively ranked in order of most (largest value) to least (smallest value) &quot;of interest&quot;&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;If the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&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;If the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&lt;/p&gt;</div></td></tr> </table> Tue, 19 Nov 2019 16:30:22 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza at 16:29, 19 November 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4376&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4376&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 16:29, 19 November 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l36" >Line 36:</td> <td colspan="2" class="diff-lineno">Line 36:</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;"></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;"></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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;For detailed information on using RNA-seq data sets with GSEA, [[Using_RNA-seq_Datasets_with_GSEA|please see this help page.]]</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;For detailed information on using RNA-seq data sets with GSEA, [[Using_RNA-seq_Datasets_with_GSEA|please see this help page.]]<ins class="diffchange diffchange-inline">&lt;/p&gt;</ins></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;<del class="diffchange diffchange-inline">li</del>&gt;<del class="diffchange diffchange-inline">Run GSEAPreranked</del>, <del class="diffchange diffchange-inline">if </del>the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&lt;/<del class="diffchange diffchange-inline">li&gt;</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>&lt;<ins class="diffchange diffchange-inline">p</ins>&gt; <ins class="diffchange diffchange-inline">for other data types, it is generally recommended to use GSEA-Preranked</ins>, <ins class="diffchange diffchange-inline">where the features being analyzed have been quantitatively ranked in order of most (largest value) to least (smallest value) &quot;of interest&quot;&lt;/p&gt;</ins></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><del class="diffchange diffchange-inline">&lt;/ol</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;p&gt;If </ins>the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&lt;/<ins class="diffchange diffchange-inline">p</ins>&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&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;"></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;"></td></tr> </table> Tue, 19 Nov 2019 16:29:59 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza at 16:25, 19 November 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4375&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4375&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 16:25, 19 November 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l36" >Line 36:</td> <td colspan="2" class="diff-lineno">Line 36:</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;"></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;"></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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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><del class="diffchange diffchange-inline">&lt;p&gt;GSEA requires as input an expression dataset, which contains expression profiles for multiple samples.  While the software supports multiple input file formats for these datasets, the tab-delimited [[Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29|GCT]] format is the most common.  The first column of the GCT file contains feature identifiers (genes or probes in the case of data derived from DNA microarray experiments, genes or transcripts in the case of data derived from RNA-Seq experiments).  The second column contains a description of the feature; this column is ignored by GSEA.  Subsequent columns contain the expression values for each feature, with one sample's expression profile per column.&lt;/p&gt;</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>&lt;p&gt;For <ins class="diffchange diffchange-inline">detailed </ins>information on <ins class="diffchange diffchange-inline">using </ins>RNA-seq data <ins class="diffchange diffchange-inline">sets with GSEA, </ins>[[<ins class="diffchange diffchange-inline">Using_RNA</ins>-<ins class="diffchange diffchange-inline">seq_Datasets_with_GSEA</ins>|<ins class="diffchange diffchange-inline">please see this help page.</ins>]]</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><del class="diffchange diffchange-inline">&lt;p&gt;It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived.  The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. RSEM quantification produces expression estimates in several units:&lt;/p&gt;</del></div></td><td colspan="2"> </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;ul&gt;</del></div></td><td colspan="2"> </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;li&gt;expected counts&lt;/li&gt;</del></div></td><td colspan="2"> </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;li&gt;transcripts per million (TPM)&lt;/li&gt;</del></div></td><td colspan="2"> </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;li&gt;FPKM&lt;/li&gt;</del></div></td><td colspan="2"> </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;/ul&gt;</del></div></td><td colspan="2"> </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&gt;Expression data that has been normalized to support comparisons of a feature's expression levels across samples is important for GSEA. There are RNA-seq normalization methods (e.g., TMM, geometric mean) that should be applied to the expected counts prior to the incorporation of the expression estimates into a GCT expression data file.&lt;/p&gt;</del></div></td><td colspan="2"> </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; For <del class="diffchange diffchange-inline">more </del>information on <del class="diffchange diffchange-inline">performing GSEA with </del>RNA-seq data <del class="diffchange diffchange-inline">see: </del>[[<del class="diffchange diffchange-inline">RNA</del>-<del class="diffchange diffchange-inline">Seq_Data_and_Ensembl_CHIP_files</del>|<del class="diffchange diffchange-inline">RNA-seq Data and Ensembl CHIP Files</del>]]<del class="diffchange diffchange-inline">&lt;/p&gt;</del></div></td><td colspan="2"> </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&gt;The GSEA algorithm ranks the features listed in a GCT file.  It provides a number of alternative statistics that can be used for feature ranking.  But in all cases (or at least in the cases where the dataset represents expression profiles for differing categorical phenotypes) the ranking statistics capture some measure of genes' differential expression between a pair of categorical phenotypes.  The GSEA team has yet to determine whether these ranking statistics, originally selected for their effectiveness when used with expression data derived from DNA Microarray experiments, are appropriate for use with expression data derived from RNA-seq experiments.  As an alternative to standard GSEA, analysis of data derived from RNA-seq experiments may also be conducted through the GSEAPreranked tool.&lt;/p&gt;</del></div></td><td colspan="2"> </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&gt;In particular:&lt;/p&gt;</del></div></td><td colspan="2"> </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;ol&gt;</del></div></td><td colspan="2"> </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;li&gt;Prior to conducting gene set enrichment analysis, conduct your differential expression analysis using any of the tools developed by the bioinformatics community (e.g., cuffdiff, edgeR, DESeq, etc).&lt;/li&gt;</del></div></td><td colspan="2"> </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;li&gt;Based on your differential expression analysis, rank your features and capture your ranking in an RNK-formatted file.  The ranking metric can be whatever measure of differential expression you choose from the output of your selected DE tool.  For example, cuffdiff provides the (base 2) log of the fold change.&lt;/li&gt;</del></div></td><td colspan="2"> </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;Run GSEAPreranked, if the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&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;Run GSEAPreranked, if the exact magnitude of the rank metric is not directly biologically meaningful select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&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;/ol&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;/ol&gt;</div></td></tr> </table> Tue, 19 Nov 2019 16:25:27 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Helga at 23:48, 13 November 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4362&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4362&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 23:48, 13 November 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l241" >Line 241:</td> <td colspan="2" class="diff-lineno">Line 241:</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;MsoListContinue&quot;&gt;Many IT organizations block the use of FTP of their networks, making it impossible to reach these files.  We recommend downloading the files from our website (available either individually or as full ZIP bundles) and then bringing them into GSEA via the Load Data screen.  Note that you will need to look for the local file options in the Run GSEA file choosers.</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;MsoListContinue&quot;&gt;Many IT organizations block the use of FTP of their networks, making it impossible to reach these files.  We recommend downloading the files from our website (available either individually or as full ZIP bundles) and then bringing them into GSEA via the Load Data screen.  Note that you will need to look for the local file options in the Run GSEA file choosers.</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><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">&lt;h4&gt;What version of R do I need for the GSEA-R software?&lt;/h4&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">&lt;p class=&quot;MsoListContinue&quot;&gt;&lt;span style=&quot;&quot;&gt;&amp;nbsp;&lt;/span&gt;It was written for version 1.9 but has not been updated since 2005 and may not work as-is with modern R distributions.  This implementation is intended for experienced computational biologists who want to tweak and play with the algorithm.&lt;/p&gt;</del></div></td><td colspan="2"> </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;"></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;"></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;h4&gt;How do I add GSEA to my microarray analysis pipeline?&lt;/h4&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;h4&gt;How do I add GSEA to my microarray analysis pipeline?&lt;/h4&gt;</div></td></tr> </table> Wed, 13 Nov 2019 23:48:00 GMT Helga https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza: correction to preranked weighting recommendation https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4353&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4353&oldid=prev <p>correction to preranked weighting recommendation</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 14:16, 3 October 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l50" >Line 50:</td> <td colspan="2" class="diff-lineno">Line 50:</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;Prior to conducting gene set enrichment analysis, conduct your differential expression analysis using any of the tools developed by the bioinformatics community (e.g., cuffdiff, edgeR, DESeq, etc).&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;Prior to conducting gene set enrichment analysis, conduct your differential expression analysis using any of the tools developed by the bioinformatics community (e.g., cuffdiff, edgeR, DESeq, etc).&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;li&gt;Based on your differential expression analysis, rank your features and capture your ranking in an RNK-formatted file.  The ranking metric can be whatever measure of differential expression you choose from the output of your selected DE tool.  For example, cuffdiff provides the (base 2) log of the fold change.&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;Based on your differential expression analysis, rank your features and capture your ranking in an RNK-formatted file.  The ranking metric can be whatever measure of differential expression you choose from the output of your selected DE tool.  For example, cuffdiff provides the (base 2) log of the fold change.&lt;/li&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;li&gt;Run GSEAPreranked, <del class="diffchange diffchange-inline">but make sure to </del>select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&lt;/li&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;li&gt;Run GSEAPreranked, <ins class="diffchange diffchange-inline">if the exact magnitude of the rank metric is not directly biologically meaningful </ins>select &quot;classic&quot; for your enrichment score (thus, not weighting each gene's contribution to the enrichment score by the value of its ranking metric).&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;/ol&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;/ol&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&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;Please note that if you choose to use any of the gene sets available from MSigDB in your analysis, you need to make sure that the features listed in your RNK file are genes, and the genes are identified by their HUGO gene symbols.  All gene symbols listed in the RNK file must be unique, and we recommend the values of the ranking metrics be unique.&lt;/p&gt;</div></td></tr> </table> Thu, 03 Oct 2019 14:16:59 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Eby at 06:41, 22 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4332&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4332&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 06:41, 22 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l248" >Line 248:</td> <td colspan="2" class="diff-lineno">Line 248:</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;If you are using GenePattern pipelines ([http://www.GenePattern.org/ http://www.GenePattern.org/]), GSEA is available as a GenePattern analysis module.&lt;br /&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;If you are using GenePattern pipelines ([http://www.GenePattern.org/ http://www.GenePattern.org/]), GSEA is available as a GenePattern analysis module.&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;If you are implementing your own microarray analysis pipeline, GSEA can be run from the command line. Use full file specifications <del class="diffchange diffchange-inline">and the &lt;span style=&quot;font-family: courier new;&quot;&gt;-Dhome&lt;/span&gt; parameter </del>to ensure that you are reading data from and writing data to the desired locations. For more information, see [http://<del class="diffchange diffchange-inline">www</del>.broadinstitute.org/gsea/<del class="diffchange diffchange-inline">doc</del>/<del class="diffchange diffchange-inline">GSEAUserGuideFrame</del>.<del class="diffchange diffchange-inline">html?Running_Command_Line Running GSEA from </del>the <del class="diffchange diffchange-inline">Command Line</del>] <del class="diffchange diffchange-inline">in the &lt;span style=&quot;font-style: italic;&quot;&gt;GSEA User Guide&lt;/span&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&gt;If you are implementing your own microarray analysis pipeline, GSEA can be run from the command line. Use full file specifications to ensure that you are reading data from and writing data to the desired locations. For more information, see [http://<ins class="diffchange diffchange-inline">software</ins>.broadinstitute.org<ins class="diffchange diffchange-inline">/cancer/software</ins>/gsea/<ins class="diffchange diffchange-inline">wiki/index.php</ins>/<ins class="diffchange diffchange-inline">FAQ#How_do_I_run_GSEA_from_the_command_line</ins>.<ins class="diffchange diffchange-inline">3F </ins>the <ins class="diffchange diffchange-inline">FAQ item above</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;h4&gt;Do I have to be connected to the internet to run GSEA software?&lt;/h4&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;h4&gt;Do I have to be connected to the internet to run GSEA software?&lt;/h4&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;MsoListBullet&quot;&gt;No. If you download the GSEA desktop application .jar file, you can use most functions in GSEA without being connected to the internet; for example, you can load files, run analyses, and review analysis results. However:&lt;br /&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;MsoListBullet&quot;&gt;No. If you download the GSEA desktop application .jar file, you can use most functions in GSEA without being connected to the internet; for example, you can load files, run analyses, and review analysis results. However:&lt;br /&gt;</div></td></tr> </table> Thu, 22 Aug 2019 06:41:22 GMT Eby https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Eby at 06:32, 22 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4331&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4331&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 06:32, 22 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l213" >Line 213:</td> <td colspan="2" class="diff-lineno">Line 213:</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>From the GSEA website, the GSEA desktop application can be launched with 1, 2, 4, or 8 GB of memory. Use the dropdown menu above the launch button to specify the amount. Note that 32-bit Java will not support greater than 2 GB.</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>From the GSEA website, the GSEA desktop application can be launched with 1, 2, 4, or 8 GB of memory. Use the dropdown menu above the launch button to specify the amount. Note that 32-bit Java will not support greater than 2 GB.</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>When running GSEA from <del class="diffchange diffchange-inline">a .jar file downloaded from the website</del>, you can <del class="diffchange diffchange-inline">specify </del>the memory on <del class="diffchange diffchange-inline">the </del>command <del class="diffchange diffchange-inline">line by using </del>the -Xmx <del class="diffchange diffchange-inline">flag</del>. <del class="diffchange diffchange-inline">For example</del>&lt;<del class="diffchange diffchange-inline">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>When running GSEA from <ins class="diffchange diffchange-inline">one of our downloadable bundles</ins>, you can <ins class="diffchange diffchange-inline">increase </ins>the memory <ins class="diffchange diffchange-inline">specification by editing the launcher file.  This is &lt;tt&gt;gsea.bat&lt;/tt&gt; on Windows, &lt;tt&gt;gsea.sh&lt;/tt&gt; or &lt;tt&gt;gsea-hidpi.sh&lt;/tt&gt; </ins>on <ins class="diffchange diffchange-inline">Linux, or &lt;tt&gt;gsea.</ins>command<ins class="diffchange diffchange-inline">&lt;/tt&gt; on Mac.  Modify </ins>the <ins class="diffchange diffchange-inline">&lt;tt&gt;</ins>-Xmx<ins class="diffchange diffchange-inline">&lt;/tt&gt; setting as desired; for example, to use an 8 GB memory configuration this could be set to &lt;tt&gt;-Xmx8g&lt;/tt&gt;</ins>.</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;tt&gt;<del class="diffchange diffchange-inline">java </del>-<del class="diffchange diffchange-inline">Xmx1024m </del>-<del class="diffchange diffchange-inline">jar </del>gsea.<del class="diffchange diffchange-inline">jar</del>&lt;/tt&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;<ins class="diffchange diffchange-inline">/p</ins>&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><ins class="diffchange diffchange-inline">&lt;p&gt;The same is true of the </ins>&lt;tt&gt;<ins class="diffchange diffchange-inline">gsea</ins>-<ins class="diffchange diffchange-inline">cli.sh&lt;/tt&gt; and &lt;tt&gt;gsea-cli.bat&lt;/tt&gt; scripts for command-line usage.  Note that it's also possible to edit the JNLP files in a similar way to create an even larger Java Web Start memory configuration.&lt;/p&gt;</ins></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> </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><ins class="diffchange diffchange-inline">&lt;p&gt;For users of the Mac.app it is not easily possible to modify the memory configuration at this time.  This is a known issue that we will aim to address in a future release.  If a higher memory configuration is absolutely required, we suggest using the command</ins>-<ins class="diffchange diffchange-inline">line bundle with your own (separate) Java 11 installation.  The &lt;tt&gt;</ins>gsea.<ins class="diffchange diffchange-inline">command</ins>&lt;/tt<ins class="diffchange diffchange-inline">&gt; script is still available for launching the GUI from this bundle.&lt;br /</ins>&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><del style="font-weight: bold; text-decoration: none;">&lt;p&gt;Please note the following:&lt;/p&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">&lt;ul&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">    &lt;li&gt;Check that you are using the correct .jar file&lt;/li&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">    &lt;li&gt;Be sure to run the Java command from the folder that contains the .jar file or specify the full path to the .jar file&lt;/li&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">    &lt;li&gt;For more information about using GSEA from the command line, refer to </del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">    [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?_Running_GSEA_from_the%20Command%20Line Runnig Running GSEA from the Command Line] in the &lt;i&gt;User Guide&lt;/i&gt;&lt;/li&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">    &lt;li&gt;There are some special considerations for Windows users; see [[Windows_Launching_Issues|Windows Launching Issues]] for more information.&lt;/li&gt;</del></div></td><td colspan="2"> </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 style="font-weight: bold; text-decoration: none;">&lt;/ul&gt;</del></div></td><td colspan="2"> </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;"></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;"></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;h4&gt;How do I run GSEA from the command line?&lt;/h4&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;h4&gt;How do I run GSEA from the command line?&lt;/h4&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;<del class="diffchange diffchange-inline">See [http://www</del>.<del class="diffchange diffchange-inline">broadinstitute</del>.<del class="diffchange diffchange-inline">org</del>/<del class="diffchange diffchange-inline">gsea/doc/GSEAUserGuideFrame.html?Running_Command_Line Running GSEA from </del>the Command <del class="diffchange diffchange-inline">Line] in the </del>&lt;em <del class="diffchange diffchange-inline">style=&quot;&quot;</del>&gt;GSEA <del class="diffchange diffchange-inline">User Guide</del>&lt;/<del class="diffchange diffchange-inline">em</del>&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;<ins class="diffchange diffchange-inline">As of GSEA 4.0.0, there is a dedicated bundle available from our Downloads page for command-line usage; please refer to the included README file for an explanation of the command-line launcher script</ins>. <ins class="diffchange diffchange-inline"> Note that a separate Java 11 installation is required</ins>.<ins class="diffchange diffchange-inline">&lt;</ins>/<ins class="diffchange diffchange-inline">p&gt;</ins></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> </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><ins class="diffchange diffchange-inline">&lt;p&gt;See </ins>the <ins class="diffchange diffchange-inline">&lt;em&gt;</ins>Command&lt;<ins class="diffchange diffchange-inline">/</ins>em&gt; <ins class="diffchange diffchange-inline">feature of the various </ins>GSEA <ins class="diffchange diffchange-inline">Desktop GUI screens for example constructions of command-lines.  This is by far the easiest way to understand the various flags and options.</ins>&lt;/<ins class="diffchange diffchange-inline">p&gt;</ins></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> </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><ins class="diffchange diffchange-inline">&lt;p</ins>&gt;<ins class="diffchange diffchange-inline">The Linux bundle contains exactly the same launcher script and README along with an embedded OpenJDK 11 JVM, so there's no need for a separate download for users on that platform</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> <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;h4&gt;What version of Java do I need for the GSEA desktop software?&lt;/h4&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;h4&gt;What version of Java do I need for the GSEA desktop software?&lt;/h4&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;<del class="diffchange diffchange-inline">Java 8 is required for </del>GSEA <del class="diffchange diffchange-inline">3</del>.0 and <del class="diffchange diffchange-inline">newer.&amp;nbsp; </del>Java <del class="diffchange diffchange-inline">6 and 7 are </del>no longer <del class="diffchange diffchange-inline">recommended</del>. &lt;<del class="diffchange diffchange-inline">strong</del>&gt;<del class="diffchange diffchange-inline">Oracle </del>Java is <del class="diffchange diffchange-inline">recommended as there are known issues when running with </del>OpenJDK<del class="diffchange diffchange-inline">.  Java 9 and higher are not supported at this time&lt;/strong&gt;</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;</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><ins class="diffchange diffchange-inline">As of </ins>GSEA <ins class="diffchange diffchange-inline">4.0</ins>.0<ins class="diffchange diffchange-inline">, the various platform-specific bundles (for Windows, Mac, </ins>and <ins class="diffchange diffchange-inline">Linux) include an embedded OpenJDK 11 JVM, meaning a separate </ins>Java <ins class="diffchange diffchange-inline">installation is </ins>no longer <ins class="diffchange diffchange-inline">required for most users</ins>.</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;<ins class="diffchange diffchange-inline">/p</ins>&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><ins class="diffchange diffchange-inline">&lt;p&gt;</ins></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>Java <ins class="diffchange diffchange-inline">8 </ins>is <ins class="diffchange diffchange-inline">required for use of the Java Web Start JNLP launchers (</ins>OpenJDK <ins class="diffchange diffchange-inline">8 is fine)</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> <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;"></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;"></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l235" >Line 235:</td> <td colspan="2" class="diff-lineno">Line 238:</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;MsoListContinue&quot;&gt;Yes.  This is likely due to recent updates by Oracle, Microsoft, and browser vendors changing the version of Java on your computer.  See [[Windows_Launching_Issues|Windows Launching Issues]] for some possible solutions.&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;MsoListContinue&quot;&gt;Yes.  This is likely due to recent updates by Oracle, Microsoft, and browser vendors changing the version of Java on your computer.  See [[Windows_Launching_Issues|Windows Launching Issues]] for some possible solutions.&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;"></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;"></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;h4&gt;GSEA gives me an error message that it is unable to access CHIP files on the Broad site.  How can I fix this?&lt;/h4&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;h4&gt;GSEA gives me an error message that it is unable to access CHIP <ins class="diffchange diffchange-inline">or GMT </ins>files on the Broad site.  How can I fix this?&lt;/h4&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;MsoListContinue&quot;&gt;<del class="diffchange diffchange-inline">A recent Broad </del>IT <del class="diffchange diffchange-inline">security change caused issues for some users in accessing our annotation (CHIP) files.  This was fixed in </del>the <del class="diffchange diffchange-inline">GSEA Desktop v2.2.1 update</del>, <del class="diffchange diffchange-inline">available from [http://www.broadinstitute.org/gsea/downloads.jsp our Downloads page]</del>.  We recommend <del class="diffchange diffchange-inline">that you delete any GSEA shortcuts or JNLP/Java Web Start </del>files <del class="diffchange diffchange-inline">that you have saved on your computer before downloading.  It may also be necessary to [https://www.java.com/en/download/help/plugin_cache.xml clear your Java cache] </del>from <del class="diffchange diffchange-inline">within </del>the <del class="diffchange diffchange-inline">Java Control Panel as well</del>.  <del class="diffchange diffchange-inline">Be sure </del>to <del class="diffchange diffchange-inline">select </del>the <del class="diffchange diffchange-inline">option to delete &quot;Installed Applications and Applets&quot; to fully clear </del>the <del class="diffchange diffchange-inline">cache</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;MsoListContinue&quot;&gt;<ins class="diffchange diffchange-inline">Many </ins>IT <ins class="diffchange diffchange-inline">organizations block </ins>the <ins class="diffchange diffchange-inline">use of FTP of their networks</ins>, <ins class="diffchange diffchange-inline">making it impossible to reach these files</ins>.  We recommend <ins class="diffchange diffchange-inline">downloading the </ins>files from <ins class="diffchange diffchange-inline">our website (available either individually or as full ZIP bundles) and then bringing them into GSEA via </ins>the <ins class="diffchange diffchange-inline">Load Data screen</ins>.  <ins class="diffchange diffchange-inline">Note that you will need </ins>to <ins class="diffchange diffchange-inline">look for </ins>the <ins class="diffchange diffchange-inline">local file options in </ins>the <ins class="diffchange diffchange-inline">Run GSEA file choosers</ins>.</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> <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;"></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;"></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;h4&gt;What version of R do I need for the GSEA-R software?&lt;/h4&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;h4&gt;What version of R do I need for the GSEA-R software?&lt;/h4&gt;</div></td></tr> </table> Thu, 22 Aug 2019 06:32:55 GMT Eby https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza at 17:23, 22 January 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4238&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4238&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 17:23, 22 January 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td> <td colspan="2" class="diff-lineno">Line 44:</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;p&gt;Expression data that has been normalized to support comparisons of a feature's expression levels across samples is important for GSEA. There are RNA-seq normalization methods (e.g., TMM, geometric mean) that should be applied to the expected counts prior to the incorporation of the expression estimates into a GCT expression data file.&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;Expression data that has been normalized to support comparisons of a feature's expression levels across samples is important for GSEA. There are RNA-seq normalization methods (e.g., TMM, geometric mean) that should be applied to the expected counts prior to the incorporation of the expression estimates into a GCT expression data file.&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;The GSEA algorithm ranks the features listed in a GCT file.  It provides a number of alternative statistics that can be used for feature ranking.  But in all cases (or at least in the cases where the dataset represents expression profiles for differing categorical phenotypes) the ranking statistics capture some measure of genes' differential expression between a pair of categorical phenotypes.  The GSEA team has yet to determine whether <del class="diffchange diffchange-inline">any of </del>these ranking statistics, originally selected for their effectiveness when used with expression data derived from DNA Microarray experiments, are appropriate for use with expression data derived from RNA-seq experiments.  <del class="diffchange diffchange-inline">We hopefully will be able </del>to <del class="diffchange diffchange-inline">devote some time to investigating this, but in the mean time</del>, <del class="diffchange diffchange-inline">we are recommending use of the GSEAPreranked tool for conducting gene set enrichment </del>analysis of data derived from RNA-seq experiments.&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><ins class="diffchange diffchange-inline">&lt;p&gt; For more information on performing GSEA with RNA-seq data see: [[RNA-Seq_Data_and_Ensembl_CHIP_files|RNA-seq Data and Ensembl CHIP Files]]&lt;/p&gt;</ins></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;The GSEA algorithm ranks the features listed in a GCT file.  It provides a number of alternative statistics that can be used for feature ranking.  But in all cases (or at least in the cases where the dataset represents expression profiles for differing categorical phenotypes) the ranking statistics capture some measure of genes' differential expression between a pair of categorical phenotypes.  The GSEA team has yet to determine whether these ranking statistics, originally selected for their effectiveness when used with expression data derived from DNA Microarray experiments, are appropriate for use with expression data derived from RNA-seq experiments.  <ins class="diffchange diffchange-inline">As an alternative </ins>to <ins class="diffchange diffchange-inline">standard GSEA</ins>, analysis of data derived from RNA-seq experiments <ins class="diffchange diffchange-inline">may also be conducted through the GSEAPreranked tool</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&gt;In particular:&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;In particular:&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;ol&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;ol&gt;</div></td></tr> </table> Tue, 22 Jan 2019 17:23:21 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ Acastanza: Removed incorrect guidance on use of FPKM https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4237&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=FAQ&diff=4237&oldid=prev <p>Removed incorrect guidance on use of FPKM</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 16:54, 22 January 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l37" >Line 37:</td> <td colspan="2" class="diff-lineno">Line 37:</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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;h4&gt;Can I use GSEA to analyze SNP, SAGE, ChIP-Seq or RNA-Seq data?&lt;/h4&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;GSEA requires as input an expression dataset, which contains expression profiles for multiple samples.  While the software supports multiple input file formats for these datasets, the tab-delimited [[Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29|GCT]] format is the most common.  The first column of the GCT file contains feature identifiers (genes or probes in the case of data derived from DNA microarray experiments, genes or transcripts in the case of data derived from RNA-Seq experiments).  The second column contains a description of the feature; this column is ignored by GSEA.  Subsequent columns contain the expression values for each feature, with one sample's expression profile per column.&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;GSEA requires as input an expression dataset, which contains expression profiles for multiple samples.  While the software supports multiple input file formats for these datasets, the tab-delimited [[Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29|GCT]] format is the most common.  The first column of the GCT file contains feature identifiers (genes or probes in the case of data derived from DNA microarray experiments, genes or transcripts in the case of data derived from RNA-Seq experiments).  The second column contains a description of the feature; this column is ignored by GSEA.  Subsequent columns contain the expression values for each feature, with one sample's expression profile per column.&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;It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived.  The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. <del class="diffchange diffchange-inline"> In the case of expression data derived from RNA-seq experiments, it is not required that the expression values be in units of FPKM.  </del>RSEM quantification produces expression estimates in several units:&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;It is important to note that there are no hard and fast rules regarding how a GCT file's expression values are derived.  The important point is that they are comparable to one another across features within a sample and comparable to one another across samples. RSEM quantification produces expression estimates in several units:&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;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;expected counts&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;expected counts&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l43" >Line 43:</td> <td colspan="2" class="diff-lineno">Line 43:</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;FPKM&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;FPKM&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;p&gt;Expression data <del class="diffchange diffchange-inline">in units of FPKM </del>has been normalized to support comparisons of a feature's expression levels across samples<del class="diffchange diffchange-inline">, which </del>is important for GSEA<del class="diffchange diffchange-inline">; however, there </del>are <del class="diffchange diffchange-inline">other </del>RNA-seq normalization methods (e.g., TMM, geometric mean) that <del class="diffchange diffchange-inline">could </del>be applied to the expected counts prior to the incorporation of the expression estimates into a GCT expression data file.&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;Expression data <ins class="diffchange diffchange-inline">that </ins>has been normalized to support comparisons of a feature's expression levels across samples is important for GSEA<ins class="diffchange diffchange-inline">. There </ins>are RNA-seq normalization methods (e.g., TMM, geometric mean) that <ins class="diffchange diffchange-inline">should </ins>be applied to the expected counts prior to the incorporation of the expression estimates into a GCT expression data file.&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;The GSEA algorithm ranks the features listed in a GCT file.  It provides a number of alternative statistics that can be used for feature ranking.  But in all cases (or at least in the cases where the dataset represents expression profiles for differing categorical phenotypes) the ranking statistics capture some measure of genes' differential expression between a pair of categorical phenotypes.  The GSEA team has yet to determine whether any of these ranking statistics, originally selected for their effectiveness when used with expression data derived from DNA Microarray experiments, are appropriate for use with expression data derived from RNA-seq experiments.  We hopefully will be able to devote some time to investigating this, but in the mean time, we are recommending use of the GSEAPreranked tool for conducting gene set enrichment analysis of data derived from RNA-seq experiments.&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;The GSEA algorithm ranks the features listed in a GCT file.  It provides a number of alternative statistics that can be used for feature ranking.  But in all cases (or at least in the cases where the dataset represents expression profiles for differing categorical phenotypes) the ranking statistics capture some measure of genes' differential expression between a pair of categorical phenotypes.  The GSEA team has yet to determine whether any of these ranking statistics, originally selected for their effectiveness when used with expression data derived from DNA Microarray experiments, are appropriate for use with expression data derived from RNA-seq experiments.  We hopefully will be able to devote some time to investigating this, but in the mean time, we are recommending use of the GSEAPreranked tool for conducting gene set enrichment analysis of data derived from RNA-seq experiments.&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;In particular:&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;In particular:&lt;/p&gt;</div></td></tr> </table> Tue, 22 Jan 2019 16:54:08 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:FAQ