[BioC] HGNC annotation for use in GOstats

Boel Brynedal Boel.Brynedal at ki.se
Tue Dec 10 11:02:50 CET 2013

Dear All,

I am attempting a fairly simple thing: performing a hypergeometric test for gene sets using GOstats. My gene set is in HGNC symbols as is my 'gene universe’ vector. But GOstats seems to require entrez IDs. Could anyone point me to a hgnc annotation package that includes entrez IDs? Or any other way to run GOstats using HGNC symbols. 

Thank you,

params <- new("GOHyperGParams", geneIds=geneset, universeGeneIds=universe, ontology="BP", pvalueCutoff=0.05, conditional=TRUE, testDirection="over")
> hgOver <- hyperGTest(params)
Error in eapply(ID2GO(datPkg), function(goids) { : 
  error in evaluating the argument 'env' in selecting a method for function 'eapply': Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘cols’ for signature ‘"function"’

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