Difference between revisions of "Known Issues"
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<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 />---- Full Error Message ---- <br />na <br /> ---- Stack Trace ---- <br /># of exceptions: 1 <br />------null------ <br />java.lang.OutOfMemoryError <br /><br /><span style="font-weight: bold;">Solution</span>: This is a memory issue with the gsea installer on the Mac. As a workaround, use the following command to launch <br />the GSEA application rather than double clicking the icon: <br /> <br />java -Xmx1800m xapps.gsea.Main<br /><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 />---- Full Error Message ---- <br />na <br /> ---- Stack Trace ---- <br /># of exceptions: 1 <br />------null------ <br />java.lang.OutOfMemoryError <br /><br /><span style="font-weight: bold;">Solution</span>: This is a memory issue with the gsea installer on the Mac. As a workaround, use the following command to launch <br />the GSEA application rather than double clicking the icon: <br /> <br />java -Xmx1800m xapps.gsea.Main<br /><br /> | ||
<h3>java.lang.NullPointerException</h3> | <h3>java.lang.NullPointerException</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 /><br />---- Stack Trace ----<br /># of exceptions: 1<br />------null------<br />java.lang.NullPointerException<br /> at edu.mit.broad.genome.alg.DatasetStatsCore.calc2ClassCategoricalMetricMarkerScores(DatasetStatsCore.java:236)<br /> at edu.mit.broad.genome.alg.markers.PermutationTestBuilder.<init>(PermutationTestBuilder.java:94)<br /> at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:360)<br /> at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:291)<br /> at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156)<br /> at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130)<br /> at xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:103)<br /> at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:137)<br /> at xtools.gsea.Gsea.execute(Gsea.java:111)<br /> at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:468)<br /> at java.lang.Thread.run(Unknown Source)<br /><br /><span style="font-weight: bold;">Solution</span>: Use gene_set permutation rather than phenotype permutation. For more information, see the description of the <em>Permutation type</em> parameter on the [http://www.broad.mit.edu/cancer/software/ | + | <span style="font-weight: bold;">Problem</span>: By default, a gene set enrichment analysis uses phenotype permutations. If you have too few samples for phenotype permutation, the following error occurs:<br /> |
| + | <br /> | ||
| + | ---- Stack Trace ----<br /> | ||
| + | # of exceptions: 1<br /> | ||
| + | ------null------<br /> | ||
| + | java.lang.NullPointerException<br /> | ||
| + | at edu.mit.broad.genome.alg.DatasetStatsCore.calc2ClassCategoricalMetricMarkerScores(DatasetStatsCore.java:236)<br /> | ||
| + | at edu.mit.broad.genome.alg.markers.PermutationTestBuilder.<init>(PermutationTestBuilder.java:94)<br /> | ||
| + | at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:360)<br /> | ||
| + | at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:291)<br /> | ||
| + | at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:156)<br /> | ||
| + | at edu.mit.broad.genome.alg.gsea.KSTests.executeGsea(KSTests.java:130)<br /> | ||
| + | at xtools.gsea.AbstractGsea2Tool.execute_one(AbstractGsea2Tool.java:103)<br /> | ||
| + | at xtools.gsea.AbstractGsea2Tool.execute_one_with_reporting(AbstractGsea2Tool.java:137)<br /> | ||
| + | at xtools.gsea.Gsea.execute(Gsea.java:111)<br /> | ||
| + | at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:468)<br /> | ||
| + | at java.lang.Thread.run(Unknown Source)<br /> | ||
| + | <br /> | ||
| + | <span style="font-weight: bold;">Solution</span>: 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/cancer/software/gsea/doc/GSEAUserGuideFrame.htm?Run_GSEA_Page Run GSEA Page] in the <em style="">GSEA User Guide</em>. | ||
Revision as of 13:39, 10 January 2007
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.
