I'm trying to used the results of a differential expression analysis to look for enriched genes using goseq but I'm having a beast of a time even getting a trial for my non-native species working.
- downloaded gene lengths as a numeric vector taken from biomart (Length)
- A gene.vector created from all of the surveyed genes with 1 or 0 depending on DE (from my output file named DE)
- A dataframe containing gene ids and the associated GO terms taken from biomart (Named GOT)
My test code:
assayed.genes=DE$assayed.genes de.genes=DE$de.genes gene.vector=as.integer(assayed.genes%in%de.genes) names(gene.vector)=assayed.genes Length = LEN$genelength head(gene.vector)
and I see output like
When I try to make the pwf and run goseq
pwf = nullp(gene.vector, bias.data=Length) go = goseq(pwf, gene2cat = GOT)
The pwf works and produces a plot but when I run goseq I get hit with an infinite recursion error:
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
"Error during wrapup:" repeated
Tweaks and googling haven't turned anything up, so I was hoping someone might be able to spot a glaring error in my approach or offer advice.