Question: Error topGO printGenes
0
15 months ago by
irving.jgalo230 wrote:

Hi, I want to extract the enriched genes from the significative GO terms with the printGenes function.

goID <- "GO:0005730"

gt <- printGenes(GOdata, whichTerms = goID,

chip = "org.At.tair.db", numChar = 40)

But when I run the script I get the following error:

Error in data.frame(LL.id = as.integer(unlist(mget(all.genes, envir = LL.lib,  :
arguments imply differing number of rows: 255, 444

According to that node I have 243 of 255 genes annotated

I hope you can help me

Regards

topgo • 341 views
written 15 months ago by irving.jgalo230

Could you provide how did you create your GOdata? This way the example is reproducible and I can check how to solve it. Thanks

Thanks for your time, that's how I built my Godata

GOdata  <- new ("topGOdata", ontology = "CC",
allGenes = all_pvlue , geneSel = topDiffGenes,
description = "Arabidopsis_Genes", nodeSize = 10,
annot = annFUN.org, mapping = "org.At.tair.db")

Regards

you don't pass a function to geneSel, do you?

Could you paste the output of print(GOdata)?