Known Issues

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<a href="http://www.broad.mit.edu/gsea/">GSEA Home</a> |  <a href="http://www.broad.mit.edu/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broad.mit.edu/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broad.mit.edu/gsea/contact.jsp">Contact</a>  <br />
+
<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> |  <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>  <br />
<br />
<br />
<h1>GSEA version 2</h1>
<h1>GSEA version 2</h1>
<h3>OutOfMemoryError when running GSEA</h3>
<h3>OutOfMemoryError when running GSEA</h3>
<p><strong>Problem</strong>: When running an analysis in GSEA. the following error occurs:</p>
<p><strong>Problem</strong>: When running an analysis in GSEA. the following error occurs:</p>
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<p><tt>
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<p><tt>        ---- Stack Trace ----<br />
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         ---- Stack Trace ----<br>
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# of exceptions: 1<br />
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      # of exceptions: 1<br >
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------Java heap space------<br />
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      ------Java heap space------<br>
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java.lang.OutOfMemoryError: Java heap space        </tt> </p>
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      java.lang.OutOfMemoryError: Java heap space
+
<p><strong>Cause</strong>: The error is either due to improper memory allocation,         or because you have reached the limits on your machine. </p>
-
         </tt>
+
<p><strong>Solutions</strong>:        </p>
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</p>
+
<ol>
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+
    <li>Start GSEA by clicking the <span style="font-variant: small-caps;">Launch</span>  button on the                       [http://www.broad.mit.edu/gsea/downloads.jsp Downloads] page of the GSEA web site.</li>
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<p><strong>Cause</strong>: The error is either due to improper memory allocation,  
+
    <li>Run GSEA on a more powerful computer.</li>
-
      or because you have reached the limits on your machine.
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    <li>Use no more than 1,000 permutations.</li>
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</p>
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    <li>First, collapse gene identifiers to symbols using                     [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideTEXT.htm#_Chip2Chip_Page Chip2Chip] tool,                    then run GSEA on the collapsed data set.                    <br />
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+
    When running GSEA on the collapsed dataset, make sure that <tt>'Collapse dataset(s)' = false</tt></li>
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<p><strong>Solutions</strong>:
+
    <li>When                       [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from running GSEA from the command line],                       use the <tt>-Xmx</tt> option to specify sufficient maximum amount of memory for the program.</li>
-
         <ol>
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</ol>
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            <li>Start GSEA by clicking the <span style="font-variant:small-caps">Launch</span>  button on the  
+
<p>&nbsp;</p>
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                    [http://www.broad.mit.edu/gsea/downloads.jsp Downloads] page of the GSEA web site.</li>
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<hr width="100%" size="2" hr="" />
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            <li>Run GSEA on a more powerful computer.</li>
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            <li>Use no more than 1,000 permutations.</li>
+
-
            <li>First, collapse gene identifiers to symbols using  
+
-
                    [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideTEXT.htm#_Chip2Chip_Page Chip2Chip] tool,
+
-
                     then run GSEA on the collapsed data set.
+
-
                     <br>
+
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                    When running GSEA on the collapsed dataset, make sure that <tt>'Collapse dataset(s)' = false</tt></li>
+
-
            <li>When  
+
-
                    [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from running GSEA from the command line],  
+
-
                    use the <tt>-Xmx</tt> option to specify sufficient maximum amount of memory for the program.</li>
+
-
          </ol>
+
-
</p>
+
-
<hr width="100%" size="2" /hr>
+
-
 
+
<h3>Error in memory.size when running GSEA-R</h3>
<h3>Error in memory.size when running GSEA-R</h3>
-
<p><strong>Problem</strong>: When running the example programs provided for R, the following error occurs:
+
<p><strong>Problem</strong>: When running the example programs provided for R, the following error occurs: </p>
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</p>
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<p><tt>        [1] &quot; *** Running GSEA Analysis...&quot;<br />
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<p><tt>
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Error in memory.size(size) : don't be silly!: your machine has a 4Gb address limit        </tt> </p>
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         [1] &quot; *** Running GSEA Analysis...&quot;<br>
+
-
        Error in memory.size(size) : don't be silly!: your machine has a 4Gb address limit
+
-
         </tt>
+
-
</p>
+
<p><strong>Cause</strong>: This is produced by the following line early in the GSEA.1.R file:</p>
<p><strong>Cause</strong>: This is produced by the following line early in the GSEA.1.R file:</p>
<p><tt> memory.limit(6000000000)</tt></p>
<p><tt> memory.limit(6000000000)</tt></p>
<p> This line set the memory limit to a large size as a work around to a platform problem with an earlier R version.</p>
<p> This line set the memory limit to a large size as a work around to a platform problem with an earlier R version.</p>
-
<p><strong>Solution</strong>: The easiest fix is just to comment out that line:<br /></p>
+
<p><strong>Solution</strong>: The easiest fix is just to comment out that line:<br />
 +
</p>
<p><tt> #      memory.limit(6000000000)</tt></p>
<p><tt> #      memory.limit(6000000000)</tt></p>
<p> This will allocate the default amount of memory. If after this change the program runs out of memory, change the line to:</p>
<p> This will allocate the default amount of memory. If after this change the program runs out of memory, change the line to:</p>
<p><tt> memory.limit(max. size in Mbytes available)</tt></p>
<p><tt> memory.limit(max. size in Mbytes available)</tt></p>
<hr width="100%" size="2" />
<hr width="100%" size="2" />
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<h3>Warning ('\%' is an unrecognized escape) when running GSEA-R</h3>
<h3>Warning ('\%' is an unrecognized escape) when running GSEA-R</h3>
<p><strong>Problem: </strong>When running the example programs provided for R, the following warnings occur:</p>
<p><strong>Problem: </strong>When running the example programs provided for R, the following warnings occur:</p>
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<p><tt>
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<p><tt>              1: '\%' is an unrecognized escape in a character string<br />
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               1: '\%' is an unrecognized escape in a character string<br>
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2: unrecognized escape removed from &quot;Tag \%&quot;<br />
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              2: unrecognized escape removed from &quot;Tag \%&quot;<br>
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3: '\%' is an unrecognized escape in a character string<br />
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              3: '\%' is an unrecognized escape in a character string<br>
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4: unrecognized escape removed from &quot;Gene \%&quot;<br />
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              4: unrecognized escape removed from &quot;Gene \%&quot;<br>
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5: '\%' is an unrecognized escape in a character string<br />
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              5: '\%' is an unrecognized escape in a character string<br>
+
6: unrecognized escape removed from &quot;\%&quot;<br />
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              6: unrecognized escape removed from &quot;\%&quot;<br>
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7: '\%' is an unrecognized escape in a character string<br />
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              7: '\%' is an unrecognized escape in a character string<br>
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8: unrecognized escape removed from &quot; \%)&quot;<br />
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              8: unrecognized escape removed from &quot; \%)&quot;<br>
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9: '\.' is an unrecognized escape in a character string<br />
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              9: '\.' is an unrecognized escape in a character string<br>
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10: '\.' is an unrecognized escape in a character string<br />
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              10: '\.' is an unrecognized escape in a character string<br>
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11: unrecognized escapes removed from &quot;\.report\.&quot;<br />
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              11: unrecognized escapes removed from &quot;\.report\.&quot;<br>
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12: '\.' is an unrecognized escape in a character string<br />
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              12: '\.' is an unrecognized escape in a character string<br>
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13: '\.' is an unrecognized escape in a character string<br />
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              13: '\.' is an unrecognized escape in a character string<br>
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14: unrecognized escapes removed from &quot;\.report\.&quot;<br />
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              14: unrecognized escapes removed from &quot;\.report\.&quot;<br>
+
15: '\.' is an unrecognized escape in a character string<br />
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              15: '\.' is an unrecognized escape in a character string<br>
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16: unrecognized escape removed from &quot;\.&quot;        </tt> </p>
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              16: unrecognized escape removed from &quot;\.&quot;
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<p><strong>Solution: </strong> You can ignore these warning messages.          They occur when you have R version 2.5 and higher installed. </p>
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         </tt>
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<hr width="100%" size="2" />
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</p>
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<p><strong>Solution: </strong> You can ignore these warning messages.
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         They occur when you have R version 2.5 and higher installed.
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</p>
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<hr width="100%" size="2" >
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<h3>Firewall / FTP connection issues for CHIP annotations or Gene Set Databases</h3>
<h3>Firewall / FTP connection issues for CHIP annotations or Gene Set Databases</h3>
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<p><strong>Problem</strong>:
+
<p><strong>Problem</strong>:          When you try to access the <strong>CHIP</strong> annotation files or the <strong>Gene Set Database</strong> /           <strong>MSigDB Browser</strong>, you see an error to the effect: </p>
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         When you try to access the <strong>CHIP</strong> annotation files or the <strong>Gene Set Database</strong> /  
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        <strong>MSigDB Browser</strong>, you see an error to the effect:
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</p>
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<p><font color="#ff0000">&quot;Error listing Broad website//&nbsp; Connection reset//&quot;</font></p>
<p><font color="#ff0000">&quot;Error listing Broad website//&nbsp; Connection reset//&quot;</font></p>
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<p><strong>Cause</strong>:
+
<p><strong>Cause</strong>:          This is probably because you are behind a network firewall or someother network configuration that prevents you           from accessing FTP servers on port 500. The Broad chip files and gene sets are placed on a publically accessible Broad FTP server.           The GSEA Java Desktop program tries to access the Broad FTP site to provide you easy access to the files but the network           configuration blocks access. </p>
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         This is probably because you are behind a network firewall or someother network configuration that prevents you  
+
<p><strong>Solutions:</strong><br />
-
        from accessing FTP servers on port 500. The Broad chip files and gene sets are placed on a publically accessible Broad FTP server.  
+
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        The GSEA Java Desktop program tries to access the Broad FTP site to provide you easy access to the files but the network  
+
-
          configuration blocks access.
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</p>
</p>
-
<p><strong>Solutions:</strong><br>
+
<ol>
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<ol><li> See if you can temporarilly disable your firewall when using GSEA </li>
+
    <li> See if you can temporarilly disable your firewall when using GSEA </li>
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        <li>Consult with your local network administrator to see if they have any suggestions or prior experience such issues </li>
+
    <li>Consult with your local network administrator to see if they have any suggestions or prior experience such issues </li>
-
        <li>Download the .CHIP, GeneSet databases and MSigDB XML files (see below) to your local file system. <br>
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    <li>Download the .CHIP, GeneSet databases and MSigDB XML files (see below) to your local file system. <br />
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                Expand it with WinZIP and then load the files into the program as *local files* rather than over the network. <br>
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    Expand it with WinZIP and then load the files into the program as *local files* rather than over the network. <br />
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                You will also have to turn off the internet connection mode. <br>
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    You will also have to turn off the internet connection mode. <br />
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                For this, go to <tt>Preferences -> General -> </tt> and uncheck the box at <tt>'Connect over the internet'</tt><br /><br />
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    For this, go to <tt>Preferences -&gt; General -&gt; </tt> and uncheck the box at <tt>'Connect over the internet'</tt><br />
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                This  
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    <br />
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                [http://www.broad.mit.edu/gsea/resources/files_to_download_locally_on_firewall_issues.zip large ZIP file] contains ALL  
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    This                   [http://www.broad.mit.edu/gsea/resources/files_to_download_locally_on_firewall_issues.zip large ZIP file] contains ALL                   current (as of April 8, 2008) .CHIP annotations, GENE_SET databases and MSigDB.xml file.</li>
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                current (as of April 8, 2008) .CHIP annotations, GENE_SET databases and MSigDB.xml file.</li>
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</ol>
</ol>
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</p>
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<p>&nbsp;</p>
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<hr width="100%" size="2">
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<hr width="100%" size="2" />
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<h3>Error running leading edge analysis</h3>
<h3>Error running leading edge analysis</h3>
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<strong>Problem</strong>: When you select a report for leading edge analysis, the following error sometimes occurs:<br >
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<strong>Problem</strong>: When you select a report for leading edge analysis, the following error sometimes occurs:<br />
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<br><tt>
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&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; java.lang.NullPointerException<br >
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at org.genepattern.gsea.LeadingEdgeWidget.setData(EIKM)<br >
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at xapps.gsea.LeadingEdgeReportWidget.setData(EIKM)<br >
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at xapps.gsea.LeadingEdgeReportWidget$1.run(EIKM)<br >
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at java.lang.Thread.run(Unknown Source) </tt><strong><br >
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<br />
<br />
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Solution</strong>: Corrected in GSEA v2.0.1.<br >
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<tt> &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; java.lang.NullPointerException<br />
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<hr width="100%" size="2" >
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at org.genepattern.gsea.LeadingEdgeWidget.setData(EIKM)<br />
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at xapps.gsea.LeadingEdgeReportWidget.setData(EIKM)<br />
 +
at xapps.gsea.LeadingEdgeReportWidget$1.run(EIKM)<br />
 +
at java.lang.Thread.run(Unknown Source) </tt><strong><br />
 +
<br />
 +
Solution</strong>: Corrected in GSEA v2.0.1.<br />
 +
<hr width="100%" size="2" />
<h3>&quot;No probe called&quot; error in log while running GSEA</h3>
<h3>&quot;No probe called&quot; error in log while running GSEA</h3>
<p><strong>Problem</strong>: When you run GSEA, sometimes the following errors appear in the log file:</p>
<p><strong>Problem</strong>: When you run GSEA, sometimes the following errors appear in the log file:</p>
<p><tt>ERROR - No Probe called: USP9X /// USP9Y on this chip (chip name is &gt;GENE_SYMBOL&lt;)<br />
<p><tt>ERROR - No Probe called: USP9X /// USP9Y on this chip (chip name is &gt;GENE_SYMBOL&lt;)<br />
ERROR - Turning off subsequent error notifications</tt></p>
ERROR - Turning off subsequent error notifications</tt></p>
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<p><strong>Solution</strong>:  
+
<p><strong>Solution</strong>: You can ignore these errors. The three slashes (<tt>///</tt>) indicate that the chip file contains ambiguous mappings, typical for Affymetrix notation, where a probe set on the chip cannot be mapped to exactly one HUGO gene symbol. GSEA displays this error and ignores such ambigous probes.<br />
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You can ignore these errors. The three slashes (<tt>///</tt>) indicate that the chip file contains ambiguous mappings,  
+
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typical for Affymetrix notation, where a probe set on the chip cannot be mapped to exactly one HUGO gene symbol.  
+
-
GSEA displays this error and ignores such ambigous probes.<br>
+
</p>
</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
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<h1>GSEA version 1</h1>
<h1>GSEA version 1</h1>
<h3>java.lang.OutOfMemoryError (GSEA v1)</h3>
<h3>java.lang.OutOfMemoryError (GSEA v1)</h3>
<span style="font-weight: bold;">Problem</span>: On the Mac, you can run GSEA from the command line, but when you attempt to use the GSEA application from the desktop you receive errors similar to the following:<br />
<span style="font-weight: bold;">Problem</span>: On the Mac, you can run GSEA from the command line, but when you attempt to use the GSEA application from the desktop you receive errors similar to the following:<br />
-
<br /><tt>
+
<br />
-
---- Full Error Message ---- <br />
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<tt> ---- Full Error Message ---- <br />
na <br />
na <br />
---- Stack Trace ---- <br />
---- Stack Trace ---- <br />
Line 142: Line 105:
<br />
<br />
<hr width="100%" size="2" />
<hr width="100%" size="2" />
-
 
<h3>java.lang.NullPointerException (GSEA v1)</h3>
<h3>java.lang.NullPointerException (GSEA v1)</h3>
<span style="font-weight: bold;">Problem</span>: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:<br />
<span style="font-weight: bold;">Problem</span>: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:<br />
-
<br /><tt>
+
<br />
-
---- Stack Trace ----<br />
+
<tt> ---- Stack Trace ----<br />
# of exceptions: 1<br />
# of exceptions: 1<br />
------null------<br />
------null------<br />
Line 164: Line 126:
<span style="font-weight: bold;">Solution</span>: Corrected in GSEA v2. In GSEA v1, use gene_set permutation rather than phenotype permutation. For more information, see the description of the <em>Permutation type</em> parameter on the [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html?Run_GSEA_Page Run GSEA Page] in the <em style="">GSEA User Guide</em>.<br />
<span style="font-weight: bold;">Solution</span>: Corrected in GSEA v2. In GSEA v1, use gene_set permutation rather than phenotype permutation. For more information, see the description of the <em>Permutation type</em> parameter on the [http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html?Run_GSEA_Page Run GSEA Page] in the <em style="">GSEA User Guide</em>.<br />
<hr width="100%" size="2" />
<hr width="100%" size="2" />
-
 
<h1>GSEA on Linux</h1>
<h1>GSEA on Linux</h1>
<h3>Browser links do not work under Linux</h3>
<h3>Browser links do not work under Linux</h3>

Revision as of 15:10, 16 July 2009

<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> | <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>

Contents

GSEA version 2

OutOfMemoryError when running GSEA

Problem: When running an analysis in GSEA. the following error occurs:

---- Stack Trace ----

  1. of exceptions: 1

Java heap space------
java.lang.OutOfMemoryError: Java heap space

Cause: The error is either due to improper memory allocation, or because you have reached the limits on your machine.

Solutions:

  1. Start GSEA by clicking the Launch button on the Downloads page of the GSEA web site.
  2. Run GSEA on a more powerful computer.
  3. Use no more than 1,000 permutations.
  4. First, collapse gene identifiers to symbols using Chip2Chip tool, then run GSEA on the collapsed data set.
    When running GSEA on the collapsed dataset, make sure that 'Collapse dataset(s)' = false
  5. When running GSEA from the command line, use the -Xmx option to specify sufficient maximum amount of memory for the program.

 


Error in memory.size when running GSEA-R

Problem: When running the example programs provided for R, the following error occurs:

[1] " *** Running GSEA Analysis..."
Error in memory.size(size) : don't be silly!: your machine has a 4Gb address limit

Cause: This is produced by the following line early in the GSEA.1.R file:

memory.limit(6000000000)

This line set the memory limit to a large size as a work around to a platform problem with an earlier R version.

Solution: The easiest fix is just to comment out that line:

# memory.limit(6000000000)

This will allocate the default amount of memory. If after this change the program runs out of memory, change the line to:

memory.limit(max. size in Mbytes available)


Warning ('\%' is an unrecognized escape) when running GSEA-R

Problem: When running the example programs provided for R, the following warnings occur:

1: '\%' is an unrecognized escape in a character string
2: unrecognized escape removed from "Tag \%"
3: '\%' is an unrecognized escape in a character string
4: unrecognized escape removed from "Gene \%"
5: '\%' is an unrecognized escape in a character string
6: unrecognized escape removed from "\%"
7: '\%' is an unrecognized escape in a character string
8: unrecognized escape removed from " \%)"
9: '\.' is an unrecognized escape in a character string
10: '\.' is an unrecognized escape in a character string
11: unrecognized escapes removed from "\.report\."
12: '\.' is an unrecognized escape in a character string
13: '\.' is an unrecognized escape in a character string
14: unrecognized escapes removed from "\.report\."
15: '\.' is an unrecognized escape in a character string
16: unrecognized escape removed from "\."

Solution: You can ignore these warning messages. They occur when you have R version 2.5 and higher installed.


Firewall / FTP connection issues for CHIP annotations or Gene Set Databases

Problem: When you try to access the CHIP annotation files or the Gene Set Database / MSigDB Browser, you see an error to the effect:

"Error listing Broad website//  Connection reset//"

Cause: This is probably because you are behind a network firewall or someother network configuration that prevents you from accessing FTP servers on port 500. The Broad chip files and gene sets are placed on a publically accessible Broad FTP server. The GSEA Java Desktop program tries to access the Broad FTP site to provide you easy access to the files but the network configuration blocks access.

Solutions:

  1. See if you can temporarilly disable your firewall when using GSEA
  2. Consult with your local network administrator to see if they have any suggestions or prior experience such issues
  3. Download the .CHIP, GeneSet databases and MSigDB XML files (see below) to your local file system.
    Expand it with WinZIP and then load the files into the program as *local files* rather than over the network.
    You will also have to turn off the internet connection mode.
    For this, go to Preferences -> General -> and uncheck the box at 'Connect over the internet'

    This large ZIP file contains ALL current (as of April 8, 2008) .CHIP annotations, GENE_SET databases and MSigDB.xml file.

 


Error running leading edge analysis

Problem: When you select a report for leading edge analysis, the following error sometimes occurs:

                   java.lang.NullPointerException
at org.genepattern.gsea.LeadingEdgeWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget.setData(EIKM)
at xapps.gsea.LeadingEdgeReportWidget$1.run(EIKM)
at java.lang.Thread.run(Unknown Source)


Solution
: Corrected in GSEA v2.0.1.


"No probe called" error in log while running GSEA

Problem: When you run GSEA, sometimes the following errors appear in the log file:

ERROR - No Probe called: USP9X /// USP9Y on this chip (chip name is >GENE_SYMBOL<)
ERROR - Turning off subsequent error notifications

Solution: You can ignore these errors. The three slashes (///) indicate that the chip file contains ambiguous mappings, typical for Affymetrix notation, where a probe set on the chip cannot be mapped to exactly one HUGO gene symbol. GSEA displays this error and ignores such ambigous probes.

 

GSEA version 1

java.lang.OutOfMemoryError (GSEA v1)

Problem: On the Mac, you can run GSEA from the command line, but when you attempt to use the GSEA application from the desktop you receive errors similar to the following:

---- Full Error Message ----
na


Stack Trace ----
  1. of exceptions: 1

null------

java.lang.OutOfMemoryError

Solution: Corrected in GSEA v2. In GSEA v1, this is a memory issue with the gsea installer on the Mac. As a workaround, use the following command to launch the GSEA application rather than double clicking the icon:

java -Xmx1800m xapps.gsea.Main


java.lang.NullPointerException (GSEA v1)

Problem: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:

---- Stack Trace ----

  1. of exceptions: 1

null------

java.lang.NullPointerException
    at edu.mit.broad.genome.alg.DatasetStatsCore.calc2ClassCategoricalMetricMarkerScores(DatasetStatsCore.java:236)
    at edu.mit.broad.genome.alg.markers.PermutationTestBuilder.<init>(PermutationTestBuilder.java:94)
    at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:360)
    at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:291)
    at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156)
    at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130)
    at xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:103)
    at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:137)
    at xtools.gsea.Gsea.execute(Gsea.java:111)
    at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:468)
    at java.lang.Thread.run(Unknown Source)


Solution: Corrected in GSEA v2. In GSEA v1, use gene_set permutation rather than phenotype permutation. For more information, see the description of the Permutation type parameter on the Run GSEA Page in the GSEA User Guide.


GSEA on Linux

Browser links do not work under Linux

Problem: When running the GSEA desktop application under Linux, buttons and links that would normally open a browser window do not open the browser window.

Work-around: After running an analysis, you cannot click on the Success link to display the result. However, you can go to the directory that contains the analysis report output and open the index.html file in that directory.

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