Gsea enhancements

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<span style="font-weight: bold;">Note</span>: By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag <span style="color: rgb(255, 0, 255);">[Keep on enh/bug page.]</span><br /><br /><span style="font-weight: bold;">Beta testing 4/18:</span><br />1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.<br /><br />Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) 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.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)<br /><br /><span style="color: rgb(255, 102, 0);">If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.</span><br /><span style="color: rgb(255, 0, 255);">If you want to trap the error and provide a &quot;standard&quot; error box with a help button; I'm happy to write wiki text for it. Let me know<span style="font-weight: bold;">.</span></span><error details=""><span style="color: rgb(51, 153, 102);"><span style="color: rgb(0, 0, 0);" /></span></error><span style="font-weight: bold;"><error details=""><span style="color: rgb(51, 153, 102);"><br /></span></error><span style="color: rgb(255, 102, 0);"></span></span>
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<span style="font-weight: bold;">Note</span>: By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag <span style="color: rgb(255, 0, 255);">[Keep on enh/bug page.]</span><br /><br /><span style="font-weight: bold;">Beta testing 4/18:</span><br />1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.<br /><br />Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) 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.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)<br /><br /><span style="color: rgb(255, 102, 0);">If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.</span><br /><span style="color: rgb(255, 0, 255);">If you want to trap the error and provide a &quot;standard&quot; error box with a help button; I'm happy to write wiki text for it. <br /></span><error details=""><span style="color: rgb(51, 153, 102);"><span style="color: rgb(0, 0, 0);"></span></span></error><span style="font-weight: bold;"><error details=""><span style="color: rgb(51, 153, 102);"><br /></span></error><span style="color: rgb(255, 102, 0);"></span></span>

Revision as of 16:20, 24 April 2006

Note: By default the hyperlinks from the software will point to the PROD server. To make them connect to the DEV server, use the -Ddebug=true flag [Keep on enh/bug page.]

Beta testing 4/18:
1. Created a tiny dataset with 4 samples; create phenotype on the fly with 1 sample in ClassA and 3 in ClassB; got this error. If I create phenotype on the fly with 2 samples in each class, life is good.

Nan hit score for feature: TACC2 ---- Stack Trace ---- # of exceptions: 1 ------Nan hit score for feature: TACC2------ java.lang.IllegalStateException: Nan hit score for feature: TACC2 at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore_all_modes(KSCore.java:137) at edu.mit.broad.genome.alg.gsea.KSCore.calculateKSScore(KSCore.java:46) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate_canned_templates(KSTests.java:377) at edu.mit.broad.genome.alg.gsea.KSTests.shuffleTemplate(KSTests.java:292) 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.Gsea.execute_one(Gsea.java:152) at xtools.gsea.Gsea.execute(Gsea.java:104) at edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:464) at java.lang.Thread.run(Unknown Source) 2. From the command line, gene set names have to be case sensitive. They should be case INsensitive. (Tested using xtools.gsea.LeadingEdgeTool, where -gsets is comma-separated list of gene set names.)

If 2 samples or less in a class then signal to noise, tTest will not work. Need to use ratio of means.
If you want to trap the error and provide a "standard" error box with a help button; I'm happy to write wiki text for it.
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