[BioC] Gene Ontology analysis for non-affy data

Adrian Alexa adrian.alexa at gmail.com
Thu Sep 17 16:21:47 CEST 2009

Hi Yupu,

you can use topGO package with any list of genes as long as you have
the gene-to-GO mapping. You can use either Bioconductor annotation
packages or pain text files which list the gene-to-GO mapping. Look at
the manual page for "annFun" function in topGO for more information.


On Wed, Sep 16, 2009 at 11:26 PM, Yupu Liang <liang at cbio.mskcc.org> wrote:
> Hi,
> I am new to GO analysis.
> What I want to do is pretty simple: I have a list of mouse gene (gene symbol
> as ID) from illumina expression experiment and I want to found out if any GO
> term is significantly enriched among these genes.
> It seems GOstats and topGO are all designed for Affymetrix data.
> I guess I could (in theory) use GO.db to query GO,but I am afraid of
> reinventing things.
> Any suggestions?
> Thanks!
> Yupu
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