I follow along this tutorial (https://www.bioconductor.org/packages/devel/bioc/vignettes/topGO/inst/doc/topGO.pdf) to do GO enrichment analysis.
After creating the topGOdata object with
GOdata = new("topGOdata", ontology = "BP", allGenes = genelist, annot = annFUN.org, mapping = "org.At.tair.db"), I instantiate a classicCount object through
group1 <- new("classicCount", testStatistic = GOFisherTest, name = "fisher", allMembers = genes(GOdata), groupMembers = interested_genes,sigMembers = sigGenes(GOdata)).
All looks fine, however, when I check the contingency table through
contTable(group1), I got a negative number:
Then, when I run
runTest(group1), I got error :
"Error in fisher.test(contMat, alternative = "greater"): all entries of 'x' must be nonnegative and finite". Can't figure out where the problem is after googling around. Does anyone know how I could fix this?
Thank you very much!