[BioC] Gene Ontology analysis for non-affy data

Chao-Jen Wong cwon2 at fhcrc.org
Thu Sep 17 00:05:16 CEST 2009

Hi, Yopu,

I am afraid that is not true.  GOstats is not only designed for
Affymetrix, but also for other platforms (of course, including
illumina). As long as you have the annotation database, which would
allow you mapping the nuIDs (or illumina's manufacture IDs) onto
EntrezIDs, you should be able to use GOstats.

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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Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
cwon2 at fhcrc.org

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