Hello,

I have meta-transcriptomics data (RNAseq) and I used GAGE (v2.26.0) to find KEGG ortholog pathways differentially expressed. I have lists of KEGG pathways perturbed (in 1 and 2 directions)  and I want to extract significantly DE gene list (in the same way as DAVID output). So, I use essGene function but sometimes I have no genes for a pathway with p.val < 0.1. I use same options in gage and essGene function as you can see in this extract of my code :

RESgage.kegg.genus.both <- gage(exprs=ExpressionData.ko.genus, gsets=kegg.sets.ko, ref=lf, samp=lt, compare = "paired", same.dir = FALSE )
output.bidir=RESgage.kegg.genus.both.select[RESgage.kegg.genus.both.select$p.val < 0.1, 1:5]
  listPathway=rownames(output.bidir)
  geneSet<-vector(mode = "character",length = length(listPathway))
  for (j in 1:length(listPathway)){
    termselec=listPathway[j]
    gs=unique(unlist(kegg.sets.ko[termselec]))
    essData = essGene(gs, ExpressionData.ko.genus, ref=lf, samp=lt,  compare= "paired")
    essDataList=rownames(essData)
    geneSet[j] <- toString(essDataList)
  } 
  output.bidir=cbind(output.bidir, geneSet)

If I set use.fold=FALSE in essGene, I obtain genes but I want DE genes considered by gage function. Can you help me ?

I don't understand how gage function can considere a pathway perturbed without gene significantly changed.