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

[J.delasHeras at ed.ac.uk]

Hi Joern,

many thanks for that. That sounds encouraging. I'll spend some time  
with topGO tomorrow and see if I can get it to work for me.

Jose

Quoting Joern Toedling <Joern.Toedling at curie.fr>:

> 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
>
>
>



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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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