[BioC] Redundant gene sets & gagePipe

[Luo Weijun]

Christian,
You may check and remove the potential redundancy using esset.grp function on individual GAGE runs. Such redundancy processing has not been incorporated into the gagePipe procedure as it may not always be desirable for the users. 
Below is a function I wrote (warning: not fully tested!) to process the output of your gagePipe procedure. The arguments here follow the same definition of gagePipe. 
HTH
Weijun

gagePipe.esset.grp <- function(arraydata, dataname = "arraydata",
    sampnames, gsname = c("kegg.gs", "go.gs"), ref.list, samp.list,
    compare = "paired", ...) {

    load(paste(dataname, ".gage.RData", sep = ""))

    for (gs in gsname) {
        gsets = eval(as.name(paste(gs)))
        for (i in 1:length(sampnames)) {
            ref = if (is.list(ref.list))
                ref.list[[i]]
            else ref.list
            samp = samp.list[[i]]
            gage.p = eval(as.name(paste(sampnames[i], paste(gs,
                ".p", sep = ""), sep = ".")))
            outname.up = paste(sampnames[i], paste(gs, ".up",
                sep = ""), sep = ".")
            assign(paste(sampnames[i], paste(gs, ".esg.up", sep = ""),
                sep = "."), esset.grp(gage.p$greater, arraydata,
                gsets = gsets, ref = ref, samp = samp, compare = compare,
                test4up = T, output = T, outname = outname.up,
                make.plot = F, ...))

            outname.dn = paste(sampnames[i], paste(gs, ".dn",
                sep = ""), sep = ".")
            assign(paste(sampnames[i], paste(gs, ".esg.dn", sep = ""),
                sep = "."), esset.grp(gage.p$less, arraydata,
                gsets = gsets, ref = ref, samp = samp, compare = compare,
                test4up = T, output = T, outname = outname.dn,
                make.plot = F, ...))
        }
    }

    save(list = objects(pattern = "esg.up$|esg.dn$"), file = paste(dataname,
        ".gage.esset.grp.RData", sep = ""))
    return(invisible(1))

}

--------------------------------------------
On Sat, 11/30/13, Christian De Santis <christian.desantis at stir.ac.uk> wrote:

 Subject: Redundant gene sets & gagePipe
 To: "bioconductor at r-project.org" <bioconductor at r-project.org>, "luo_weijun
 Date: Saturday, November 30, 2013, 8:08 AM



  
  





 Hi Weijun,
  
 Is there also a quick way to calculate the redundant
 gene-sets in batch when analysing multiple rounds of GAGE
 using gagePipe, or can this only be done individually on
 each of the contrasts?
  
 Thanks and have a nice weekend,


 Christian  
  


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