Error topGO printGenes

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irving.jgalo23 • 0

@irvingjgalo23-14252

Last seen 6.8 years ago

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 • 1.5k views

ADD COMMENT • link 6.9 years ago irving.jgalo23 • 0

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

ADD REPLY • link 6.9 years ago Lluís Revilla Sancho ▴ 760

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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

ADD REPLY • link 6.8 years ago irving.jgalo23 • 0

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

Could you paste the output of print(GOdata)?

ADD REPLY • link 6.8 years ago • updated 4.2 years ago Lluís Revilla Sancho ▴ 760