No GO-term and no ontology in goseq() output! What am I doing wrong?

Question

[Parham]

Hi all,

I am doing goseqon S. pombe RNA-seq data. Since the organism is not on SupportedGenome database I have to create the arguments from other databases. So I get this pombe GO annotation and create a data.frame with one column the GeneIDand the other GOs. I run go.hyper=goseq(gene_pwf, gene2cat = gene2go, method="Hypergeometric") but the output does not include the columns for GO-terms and ontology (BP,CC,MF). Even if I add test.cats argument, still the output is the same.I only get these columns: category, over_represented_pvalue, under_represented_pvalue, numDEInCat, numInCat. Does anybody know what am I doing wrong? If you need more information please let me know.

[Gaima Kushwaha]

Did you figure out the problem. I'm having the same kind of output.

[Parham]

Yes I could fix it but I have to see your codes in order to help. How are you running it?

Answer 1

[romain.savary.2017]

Hi all,

As there was no answer to this problem and I have been facing the same problem and found a solution, I wanted to shared this solution if this could help.

I had several time and for different non-model species this problem, that the output file did not had the ontology term column and this is for a simple reason (in my case), because GOseq does not recognized the GO term.

In other words my "gene2cat" file contained GO term, but there was an additional space at the begining of the term " GO:XXXXX" that didn't allow GOseq to recognize this term.

So if you do not have ontology term column in your output file, you probably have to check that your GO term in "gene2cat" are in the right format with no additional characters.

I hope this help,

Best,

Romain