Known Issues

java.lang.OutOfMemoryError

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 ----
# of exceptions: 1
------null------
java.lang.OutOfMemoryError

Solution: 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

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 ----
# 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: 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.