Anyone know how to get the probe set ids for the expression matrix row names BEFORE summarisation (so like 140292811, 140292812 etc.). When I load the cel files into R, the original unnormalised expression matrix has row names from 1:number of probes:
library(oligo) geneCELs <- list.celfiles(path, full.names=TRUE) affyGeneFS <- read.celfiles(geneCELs) genePS <- rma(affyGeneFS, target="probeset") featureData(genePS) <- getNetAffx(genePS, "probeset")
so I can do exprs(genePS) and get the probesets, however I want the original probes, before they are "summarised" to the probe-set level. So something like: exprs(affyGeneFS). However this gives sequential row names as I said before.
Does anyone have any ideas? Perhaps the affy package is better suited?