[BioC] Gene Ontology analysis for non-affy data

Marc Carlson mcarlson at fhcrc.org
Wed Sep 16 23:51:11 CEST 2009

Hi Yupu,

You should read the tutorial vignette for the GOstats package.  I think
it will probably show you what you need to know:

You can find the GOstats package here:


And the tutorial here:



Yupu Liang 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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