GSVA with a genesets as a list?
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Entering edit mode
9 months ago

Hello,

I am trying to run GSVA with a list of genesets (because I couldnt make it to work with a genecollection object) , but it only uses the first geneset of the list for some reason. So I used a lapply to get it to calculate the enrichment score but the problem is that it doesn't output a formal expression set object. does anybody know how I could solve that issue?

day3_gsva<-lapply(X = btmgeneset,FUN = function(x){gsva(expr=eset_matrix, 
                                                           gset.idx.list=x, 
                                                           annotation,
                                                           method="gsva",#we use the gsva method for the Enrichment scores
                                                           kcdf="Poisson",#poisson for discrete numbers
                                                           abs.ranking=FALSE,
                                                           min.sz=1,#minimal size of each genesets
                                                           max.sz=Inf,#maximal size of each genesets
                                                           parallel.sz=2,
                                                           mx.diff=TRUE,
                                                           tau=1,#tau=switch(method,gsva=1, ssgsea=0.25, NA),
                                                           ssgsea.norm=TRUE,
                                                           verbose=TRUE)})

thank you very much,

GSVA enrichment • 359 views
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