[BioC] using GSEAlm with GO geneSetCollections

Dykema, Karl Karl.Dykema at vai.org
Tue Nov 11 15:30:29 CET 2008

Hello Mark,

You may want to try PGSEA together with limma. It takes a slightly different approach than Category but this vignette should explain things adequately.


Karl Dykema
Computational Biologist
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503

Date: Mon, 10 Nov 2008 20:49:42 -0500
From: "Mark Kimpel" <mwkimpel at gmail.com>
Subject: [BioC] using GSEAlm with GO geneSetCollections
To: "Bioconductor Newsgroup" <bioconductor at stat.math.ethz.ch>
        <6b93d1830811101749k241749ddr62424a5e511a0c16 at mail.gmail.com>
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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?

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