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  • 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, 05:49 AM.

  • #2
    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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    • #3
      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, 12:49 AM.

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      • #4
        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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        • #5
          Thanks a lot!

          Comment

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