Question: Error topGO printGenes
0
gravatar for irving.jgalo23
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
ADD COMMENTlink 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

ADD REPLYlink written 15 months ago by Lluís Revilla Sancho470

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 REPLYlink written 15 months ago by irving.jgalo230

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

Could you paste the output of `print(GOdata)`?

ADD REPLYlink written 15 months ago by Lluís Revilla Sancho470

Hi, im having exactly the same problem. did you manage to solve it ?

ADD REPLYlink written 8 months ago by juanfinello0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 121 users visited in the last hour