Hi Tingzhu,

I have used these command for preparing input for RNASeq GSEA. I hope these
command works fine for you as well.
Here's the command for preparing go.sets.hs and go.subs.hs:-

1)  Prepare a tab seperated table with three coloumns( ID, GO, Type), Where
ID is geneId, GO is your GO Id and Type is MF or BP or CC.

     a <- read.table(file="your Text file",sep="\t",header=TRUE)

2) go.sets.hs

       mysplit <- split(a$ID,a$GO)
       go.sets.hs <- lapply(mysplit,as.character)
       save(go.sets.hs,file="GoSets.RData")

3) go.subs.hs

        mysplit <- split(a$ID,a$Type)
        go.subs.hs <- lapply(mysplit,as.character)
        save(go.subs.hs,file="GoSubs.RData")

Regards



On Wed, Jan 1, 2014 at 3:02 AM, Tingzhu [guest] <guest@bioconductor.org>wrote:

>
> I am working with gage for pathway and GO analysis. I have Bovine RNA-seq
> data. The gage documentation was nicely written on data preparation and
> analysis. I know I can use kegg.gsets function to generate for gene sets
> KEGG pathway for many species including Bovine. But how about gene sets for
> GO terms? I guess I can download the data from GO website and but not sure
> how to convert it to the proper format like the go.sets.hs and go.subs.hs
> sets in the Quick start examples. Any suggestions?
>
>  -- output of sessionInfo():
>
> NA
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
Reema Singh
Postdoctoral Research Assistant
College of Life Sciences
University of Dundee,
Dundee DD1 4HN, Scotland
United Kingdom

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