contTable of classicCount object contains negative number in topGO
Entering edit mode
10 months ago
liyong ▴ 80

Hello all,

I follow along this tutorial ( to do GO enrichment analysis.

After creating the topGOdata object with GOdata = new("topGOdata", ontology = "BP", allGenes = genelist, annot =, 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:enter image description here

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!

topGO enrichment GO • 276 views

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