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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Reema Singh Postdoctoral Research Assistant College of Life Sciences University of Dundee, Dundee DD1 4HN, Scotland United Kingdom [[alternative HTML version deleted]]