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 = evalas.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 = evalas.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? ? The University of Stirling has been ranked in the top 12 of UK universities for graduate employment*. 94% of our 2012 graduates were in work and/or further study within six months of graduation. *The Telegraph The University of Stirling is a charity registered in Scotland, number SC 011159.