[Bioc-devel] GSEABase::mapIdentifiers() stopped mapping identifiers

[Robert Castelo]

hi Martin,

On Wed, 2012-03-14 at 15:58 -0700, Martin Morgan wrote:
[...]

> So the answer to the original post should have been closer to 'use 
> EntrezIdentifier for org.Hs.eg.db annotations'? As in the final line of
> 
> library(Biobase)
> library(org.Hs.eg.db)
> library(GSVAdata)
> data(c2BroadSets)
> mapped_genes <- mappedkeys(org.Hs.egSYMBOL)
> exp <- matrix(rnorm(1000), nrow=100,
>      dimnames=list(mapped_genes[1:100], paste("sample", 1:10, sep="")))
> eset <- new("ExpressionSet", exprs=exp, annotation="org.Hs.eg.db")
> gsc <- mapIdentifiers(c2BroadSets, EntrezIdentifier(annotation(eset)))
> 
> class?GeneIdentifierType says AnnotationIdentifier is meant for 
> Affymetrix chip packages (there seem to be some underlying problems 
> anyway, GeneSet(eset) creates AnnotationIdentifier).

so if you revert now to the former behavior of GSEABase, how can i
programmatically derive whether the outcome of

annotation(eset)

should be the input to

AnnotationIdentifer()

or to

EntrezIdentifier()

or to any other among the *Identifier() functions described in
class?GeneIdentifierType


??


thanks,
robert.