[BioC] GOstat with replicates

[Seth Falcon]

Hi Naomi,

Naomi Altman <naomi at stat.psu.edu> writes:

> There are times when it makes sense to have genes duplicated in both 
> the universe and the set of interest - e.g. if the geneIds come from 
> BLAST hits of unigenes of an unsequenced species against the genes of 
> a sequenced species.
>
> I fiddled a bit with GOstat, but was not able to see how to change 
> the code to allow this.  (I can see where duplication was removed in 
> the gene set but not in the universe.)
> If someone could tell me where to look in the code, I would be happy 
> to contribute back the modified code allowing duplication.

I think you will want to look in the Category package where a fair
amount of the infrastructure is located for the GO-based hyperGTest.

In particular, you may want to look at .makeValidParams in
HyperGParams-accessors.R

That said, I find the duplicated gene scenario hard to understand and
would worry that the method as implemented won't give useful results.


+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
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