WCGNA empty files for GO analysis
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Entering edit mode
3.7 years ago

Hello all. I would appreciate your help with this. Im doing an WCGNA, everything is getting well but the only thing that I have a trouble is when I tried to generate a file with all my genes from each module (to perform a gene ontology analysis)

I've performed this command, it doesnt tell me there is an error, but when I open my .txt files those are all empty.

What would you could suggest for me?

Thank you so much

allLLIDs = pulmonData$gene_symbol 
intModules = unique(moduleColorsAutomatic) 
for (module in intModules)
{
  modGenes = (moduleColorsAutomatic==module) 
  modLLIDs = allLLIDs[modGenes];
  fileName = paste("LocusLinkIDs-", module, ".txt", sep="");
  cat(modLLIDs, sep="\n", file=fileName)
}

TotfileName = paste("LocusLinkIDs-all.txt", sep="");
cat(allLLIDs, sep="\n", file=TotfileName)
wgcna RNA-Seq • 651 views
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2
Entering edit mode
3.7 years ago

I've already answered it.

The problem was that the pulmonData first column was named Gene ID, I changed to gene_symbol and now it works.

Thank you!

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