Topgo Error
2
0
Entering edit mode
7.2 years ago

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)

bioconductor gene enrichment • 2.4k views
ADD COMMENT
1
Entering edit mode
7.2 years ago

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.

ADD COMMENT
0
Entering edit mode
4.9 years ago
tao2013 • 0

The same probelm. Thanks for your sharing

ADD COMMENT

Login before adding your answer.

Traffic: 2199 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6