I am currently analyzing a microarray study which was deposited on GEO. I am using the
oligo package to obtain gene level summaries after background correction.
Now I want to map all the remaining probesets to to entrez gene ids, but I wasn't sure how to do that. I found the
getProbeInfo function which seems to be exactly what I am looking for, but was not sure which
field corresponds to entrez gene id (or ensembl gene id).
This is my code so far:
file_names <- list.files("/DDAS/MA", pattern = "CEL", full.names = T) rawData <- read.celfiles(file_names) geneSummaries <- rma(rawData, target="core") probeInfo <- getProbeInfo(geneSummaries ,field= c('fid', 'fsetid', 'atom', 'transcript_cluster_id','exon_id'), target='core')
rownames(geneSummaries) returns a list which looks something like this:
"2371346" "2371474" "2371547" "2371694" "2371738" "2371873" "2372103", ...
I would very much appreciated if somebody could tell me what the correct
field name is to get the gene identifiers, or any other way how I can get gene ids from