[BioC] using GSEAlm with GO geneSetCollections

Robert Gentleman rgentlem at fhcrc.org
Tue Nov 11 06:12:31 CET 2008

Hi Mark,
  There is no direct way to do that (at least not that I can think of). Perhaps
the easiest thing to do, is to do an unconditional test, with no filtering on
p-values (or anything else).  Then separately find all leaves, and then just
subset the results for the leaves and work off of that.

 best wishes

Mark Kimpel wrote:
> I'm using a specific Affy chipset that is supported by BioC (rat2302) and
> would like to use GSEAlm to indentify GO genesets of interest (p <0.05). I
> am only interested in the GO BP ontology and only want to use the terminal
> leaves. What is the most straightforward way to achieve this? I've read the
> vignettes from GSEABase, GSEAlm, Category, and goTools and can't find a
> direct example. I suspect I am making this too hard. Suggestions? Point me
> in the correct direction?
> Thanks,
> Mark
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 15032 Hunter Court, Westfield, IN  46074
> (317) 490-5129 Work, & Mobile & VoiceMail
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> Skype:  mkimpel
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> F. Skinner
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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