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Old 09-16-2014, 02:57 AM   #1
Parharn
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Default GO dataset for s. pombe

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!

Last edited by Parharn; 09-16-2014 at 05:49 AM.
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Old 09-16-2014, 01:17 PM   #2
GenoMax
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You had asked a similar question back in June (http://seqanswers.com/forums/showthread.php?t=44116). Did the suggestions given there not work?
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Old 09-17-2014, 12:38 AM   #3
Parharn
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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.

Last edited by Parharn; 09-17-2014 at 12:49 AM.
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Old 09-17-2014, 08:43 AM   #4
bigmw
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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:
Code:
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.
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Old 09-18-2014, 07:23 AM   #5
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Thanks a lot!
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