Gsea enhancements

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Revision as of 16:20, 24 April 2006 by Hkuehn (Talk | contribs)
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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 at at at at at at xtools.gsea.Gsea.execute_one( at xtools.gsea.Gsea.execute( at$ at 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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