[BioC] GSVA with entrez ids?

[Martin Morgan]

On 03/04/2012 01:47 PM, Ed Siefker wrote:
> I have an expression set where the featureNames are already human
> entrez ids.  What annotation package should I use to run GSVA?  I
> tried org.Hs.eg.db, but I get this error:
>
>> coad_es<-gsva(entrezSet, c2BroadSets, min.sz=10, max.sz=500, verbose=TRUE)$es.obs
> Mapping identifiers between gene sets and feature names
> Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ...,
> verbose = verbose)) :
>    error in evaluating the argument 'object' in selecting a method for
> function 'GeneSetCollection': Error in get(mapName, envir = pkgEnv,
> inherits = FALSE) :
>    object 'org.Hs.egENTREZID' not found

Hi Ed --

Actually, I think this is related to a bug report on the Bioc-devel 
mailing list the other day

https://stat.ethz.ch/pipermail/bioc-devel/2012-February/003151.html
https://stat.ethz.ch/pipermail/bioc-devel/2012-March/003173.html

and a work-around is to create a self-map

   org.Hs.egENTREZID = new.env(hash=TRUE, parent=emptyenv())
   for (k in keys(org.Hs.egENSEMBL)) org.Hs.egENTREZID[[k]] = k

The underlying issue is fixed in GSEABase available with R-2.15 alpha, 
to be released at the end of the month.

Martin


>
>
> Am I doing something wrong?
>
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