GO dataset for s. pombe

[Parharn]

Hi,
I am willing to do GO analysis on my RNA-seq data from S. pombe organism. As far as I understood "gageData" package doesn't hold the data set for S. pombe. So I could find the data set on www.pombase.org, this link. But I don't know how to load this data set into my analysis. I am following this workflow, section 4. Please help me with loading the GO dataset into above mentioned workflow.

Thanks a lot!

[GenoMax]

You had asked a similar question back in June (http://seqanswers.com/forums/showthread.php?t=44116). Did the suggestions given there not work?

[Parharn]

No this one is different! The answer to the transcriptDB post helped a lot. This one is GO annotations! Aren't them different?
I have another post with more detailed information here (https://www.biostars.org/p/112790/) if that can help to elucidate my question.

[bigmw]

What you want to do is to read in and process the annotation data into a list. Each element of this list is a gene set. You can download and unzip the data from the link you provide under linux shell:

curl -O ftp://ftp.geneontology.org/pub/go/gene-associations/gene_association.pombase.gz
gunzip gene_association.pombase.gz

Then read and process the data in R like:
pombgo=read.delim("gene_association.pombase", sep="\t", head=F, skip=44)
go=split(as.character(pombgo[,2]), pombgo[,5])
here "go" is a gene set list you can use in your gage analysis.

[Parharn]

Thanks a lot!