Known Issues

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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

Solution: 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.
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)<br /><br /><br />

Firewall / FTP connection issues for CHIP annotations or Gene Set Databases with (GSEA v2)

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

Work-around: (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 file from the link 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.

This large ZIP file contains ALL current (as of March 19, 2007) .CHIP annotations, GENE_SET databases and MSigDB.xml file:

<a href="http://www.broad.mit.edu/cancer/software/gsea/resources/files_to_download_locally_on_firewall_issues.zip">www.broad.mit.edu/cancer/software/gsea/resources/files_to_download_locally_on_firewall_issues.zip</a>

We are working on a URL based access for the next release.

Error running leading edge analysis (GSEA v2)

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.


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.

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