Question: Goseq Error Loading Length Data
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gravatar for michaelsbreen1
5.8 years ago by
University of Southampton
michaelsbreen160 wrote:

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

gene R bioconductor hg19 • 1.9k views
ADD COMMENTlink modified 5.8 years ago by Alex Reynolds27k • written 5.8 years ago by michaelsbreen160
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