Hi everyone, I'm using GAGE following Deseq2 analysis on my RNAseq data. This means, the analysis is being done on log2FC. I can't see any list of transcripts related to GO terms/pathways that are being enriched. Something like the usual tools of enrichment analysis. Is there any way, I can include genes and extract them in my results?
This is the code I'm using: wt_res is name of my Deseq2 result.
Get the log2fold changes
wt_res.fc <- wt_res$log2FoldChange names(wt_res.fc) <- wt_res$entrez
Run enrichment analysis on all log2fc
fc.kegg.sigmet.p <- gage(wt_res.fc, gsets = kegg.sigmet.gs) fc.kegg.sigmet.p.up <- as.data.frame(fc.kegg.sigmet.p$greater) fc.kegg.sigmet.p.down <- as.data.frame(fc.kegg.sigmet.p$less)
Partially solved: I now can extract the list of genes in each term by following code: Extract gene list of each term
glist<-unlist(kegg.sigmet.gs["hsa04514 Cell adhesion molecules"]) aa<-glist[glist %in% names(wt_res.fc)] extrac <- mapIds(org.Hs.eg.db, aa , 'SYMBOL' , 'ENTREZID' ) write.csv(as.data.frame(extrac), file="hsa04514.csv")
But, I still can't get the genes from my dataset that mapped to this term and made it significantly enriched.