[BioC] Bug in GSVA with methods other than default?

[Jonathan Manning]

Hi Bioconductors,

I'm attempting to use GSVA (version 1.8.0) for gene set enrichment type 
analyses, in particular to access PLAGE, it having performed well in a 
fairly recent comparison: 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0079217#pone.0079217-Tomfohr1.

Unfortunately when I call the gsva() method with an ExpressionSet type 
object (specifically a LumiBatch in my case), with any 'method' 
specification other than the default I get an error like:

Error in eSco$es.obs : $ operator is invalid for atomic vectors

Digging about in the code, this /seems/ to be because the default method 
'gsva' returns a list with an 'es.obs' element, while the others return 
straight matrices. I guess the fix would be a simple conditional in that 
top gsva() method:

if (method=='gsva'){

     Biobase::exprs(eScoEset)<- eSco$es.obs

}else{

     Biobase::exprs(eScoEset)<- eSco

}


Thanks,

Jon



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