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Old 11-08-2014, 02:18 PM   #1
Parharn
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Location: Sweden

Join Date: Jul 2013
Posts: 84
Default No GO terms in goseq output

Hi,
I am doing goseq on RNA-seq data of S. pombe. Below I am showing the last few lines of calculating the enriched GOs for my up-regulated genes. In the GO.hyper_up I don't get two last columns "term" and "ontology" as it is shown in goseq manual. Does any one have any suggestions? Let me know if you need more info


Code:
> Spo.genes.Go = read.table('gene_association.pombase', sep='\t', comment='!', stringsAsFactors = F, quote="\"")
> gene2GO = data.frame(Spo.genes.Go$V2, Spo.genes.Go$V5)
> colnames(gene2GO)=c("id", "GO")
> head(gene2GO)
           id         GO
1  SPAC212.11 GO:0005634
2  SPAC212.11 GO:0043140
3  SPAC212.11 GO:0000722
4 SPAC212.08c GO:0031362
5 SPAC212.04c GO:0009897
6 SPAC212.01c GO:0009897
> GO.hyper_up=goseq(pwf_up, gene2cat = gene2GO, method="Hypergeometric")
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go-terms, goseq, rna-seq, s.pombe

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