[BioC] GOstats question

Sean Davis sdavis2 at mail.nih.gov
Wed Mar 30 13:19:14 CEST 2005

On Mar 30, 2005, at 4:03 AM, Rickman David wrote:

>  Hello,
> A naive question (I am by no means an ace R user) concerning GOstats 
> and splice variants:
> why do you rely on locuslink to map GO terms when GOA that take into 
> account splice variants as well via, for example, RefSeq?  Using the 
> GOstats tool to study Affymetrix u133a data, I noticed that thhe 
> hgu133aACCNUM mapping offers RefSeq mapping if I understand - knowing 
> that you are limited to the genbank accession number attribution for a 
> probe set offered by Affymetrix.
> Thanks for any help/comments


I'm perhaps not the best person to answer this (Robert Gentleman and 
his team are), but I think the annotation pipeline that is used for the 
bioconductor packages goes through LocusLink (Entrez Gene) in all 
cases.  Since the mapping is through LocusLink, there isn't a way to 
get back to "trancript-level" detail.


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