topGO error: KS elim test
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Entering edit mode
15 months ago
Priya Rao • 0

This is my code:

library(topGO)

hs_topGOdata <- new("topGOdata", description = "Human proteins", ontology = c("BP"), allGenes = allGenes.hs, geneSel = interestingpValues.hs, nodeSize=5, annot = annFUN.gene2GO, gene2GO = geneID2GO.hs)

resultFisher <- runTest(hs_topGOdata, algorithm = "classic", statistic = "fisher")
resultFisher

resultFisher.elim <- runTest(hs_topGOdata, algorithm = "elim", statistic = "fisher")
resultFisher.elim

resultKS <- runTest(hs_topGOdata, algorithm = "classic", statistic = "ks")
resultKS

resultKS.elim <- runTest(hs_topGOdata, algorithm = "elim", statistic = "ks")
resultKS.elim

All my other tests are running well except `resultKS.elim` which gives me the following error:

```r
Error in ks.test.default(x.a, seq_len(N)[-x.a], alternative = "greater") : 
  not enough 'y' data

I have searched for the NAs and there are no NAs!

KS topGO enrichment-analysis • 365 views
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