Goseq Error Loading Length Data

Question

[michaelsbreen1]

Hi all ,

I receive an error loading length data with GOSeq.

I have count data generated by RSEM counting to hg19. Following I used edgeR to identify DEGs. Now I am interested in using GoSeq for gene ontology of my DEG list.

In my code I create a vector and load this into the GoSeq framework.

library(goseq)
all.genes <- scan("All.txt", what=character())
de.genes <-scan("DE.txt", what=character())
genes = as.integer(all.genes %in% de.genes) 
names(genes) = all.genes 
pwf=nullp(genes,"hg19","geneSymbol")

Here is my error:

Loading hg19 length data...
Error in qr.R(qrx) : 
  could not find symbol "..." in environment of the generic function

Suggestions?

Michael