No GO terms in goseq output

Parharn · 11-08-2014, 02:18 PM

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")

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
goseq errors	mparida85	Bioinformatics	8	07-05-2014 05:20 PM
Using GOseq on Cuffdiff output	sindrle	Bioinformatics	6	03-14-2014 01:43 PM
Goseq for non-native goseq db	annaprotasio	Bioinformatics	12	03-31-2013 11:36 PM
GOseq errors	egorleg	RNA Sequencing	6	11-29-2012 02:09 PM
installing goseq	chknbio	Bioinformatics	2	05-29-2012 02:00 PM

11-08-2014, 02:18 PM	#1
Parharn Member Location: Sweden Join Date: Jul 2013 Posts: 84	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")