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

[Joern Toedling]

Hi Jose,

these packages are not limited to Affy arrays, but they may require a similar
annotation package as those provided for the Affy arrays. If you have
Entrezgene identifiers, you can use the org.Hs.eg.db (or org.Mm.eg.db, ...).
Or you could build your very own annotation package using SQLForge (package
AnnotationDbi). And at least topGO also allows you to provide the gene-to-go
relations as a simple list. You would still need to decide on the gene
universe to use, but I think that the vignettes of these package contain some
thoughts on how to do that.

Regards,
Joern

On Mon, 08 Feb 2010 16:29:48 +0000, J.delasHeras wrote
> 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
> 

---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927