I'm using topGO and getting a couple odd (maybe related?) errors.
The default test
resultWeight01 <- runTest(BP_GOdata, statistic = 'fisher')
runs fine.
But, when I try:
resultKS <- runTest(BP_GOdata, algorithm = 'classic', statistic = 'ks')
I get the message
Error in seq_len(N)[-x.a] :
only 0's may be mixed with negative subscripts
and when I run
resultKS.elim <- runTest(BP_GOdata, algorithm = 'elim', statistic = "ks")
I get the error message:
Error in ks.test(x.a, seq_len(N)[-x.a], alternative = "greater") :
not enough 'y' data
The default results may be adequate, but curious why the other methods don't work.
My topGOdata:
BP_GOdata <- new("topGOdata",
description = "BP gene set analysis", ontology = "BP",
allGenes = geneList, geneSel = selectFDR,
nodeSize = 10,
annot = annFUN.gene2GO, gene2GO = geneID2GO)
•
written
by
johnstantongeddes
2 answers
Solved my own question...
I had NA values in my 'geneList'. These didn't cause problems with the default (gene counts) but did cause problems with the 'ks' tests based on gene scores.
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