[BioC] GOstats : Error in getUniverseHelper - No Entrez Gene ids left in universe

[Benoit Ballester]

Hi,

I am getting this error when I run hyperGTest from GOstats. Any idea on 
what is going wrong would be appreciated ?

R version 2.8.1 (2008-12-22)
GOstats  1.7.4
I am also attaching the files genefile/universe.txt

write.table(ori$Accession, "universe.txt", sep = "\t", 
quote=FALSE,row.names=FALSE,col.names=FALSE)

geneFile  <- "genefile.txt"
uniFile   <- "universe.txt"

universe  <- scan(uniFile, what="character")
genelist  <- scan(geneFile, what="character")

pcut    <- 0.05
catSize <- 5


params    <- new("GOHyperGParams", geneIds=genelist, 
universeGeneIds=universe,
               annotation="org.Mm.eg", ontology="BP", pvalueCutoff=pcut,
               conditional=FALSE, testDirection="over")


results <- hyperGTest(params)
Error in getUniverseHelper(probes, datPkg, entrezIds) :
   No Entrez Gene ids left in universe




Thanks,

Ben


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