Hi all,
I've been struggling with the problem below for a few days now and am totally stumped. I am trying to use essGene to extract the data for essential member genes in my significantly differentially expressed gene sets and then geneData for the output and visualization of expression data
for these selected genes. I followed the vignette closely and have pretty much just replicated the code, but every time I run the code below I get the following error: Error in [.data.frame(gData, , icol) : undefined columns selected
Does anyone have any ideas what might be going on or how to fix this?
Many thanks,
Sarah
CODE:
cnts.kegg.p.CvsAC<- gage(cnts.norm, gsets = kegg.gs, ref = c(7:11), samp = c(13:17), compare ="unpaired", same.dir = TRUE)
rownames(cnts.kegg.p.CvsAC$greater)[1:3]
gs=uniqueunlistkegg.gs[rownames(cnts.kegg.p.CvsAC$greater)[1:3]]))
essData=essGene(gs, cnts.norm, ref = c(7:12), samp = c(13:17), compare ="unpaired")
head(essData, 10)
ref1=7:12
samp1=13:17
for (gs in rownames(cnts.kegg.p.CvsAC$greater)[1:3]) {
outname = gsub(" |:|/", "_", substr(gs, 10, 100))
geneData(genes = kegg.gs[[gs]], exprs = essData, ref = ref1, samp = samp1, outname = outname, txt = T, heatmap = T, Colv = F, Rowv = F, dendrogram = "none", limit = 3, scatterplot = T)
}
