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