[BioC] GSEA, topGO, GOstats...? what's a good way to look at GO over-representation?

[J.delasHeras at ed.ac.uk]

Dear list,

I have a few gene lists derived from a human Illumina expression  
array. I just have Illumina IDs, I have gene names, and I have entrez  
gene IDs I obtained for them.

I would like to analyse the list to look for over-representation of  
some category, probably using gene ontologies.
I see there are several packages that seem to address this, although  
when I look at the examples I get the feeling they were designed with  
Affy arrays in mind and depend on an Affy array design...

I am sure I am not the only one wanting to do this type of work on  
non-Affy arrays... I would appreciate a nudge towards the right  
package, or a way to "persuade" it to work with non-Affy array data,  
after all I imagine that all the array design is used for is the  
definition of teh genelists/universe and retrieval of the relevant GO  
ids.

Thank you for any helpful comments.

Jose

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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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