I am new in R and i trying to re-annotate some Affy cell files to Ensemle ID and then afterwards normalize the data with RMA. The problem is that as an end result in stead of having a reduced number of IDs (from the normal 54 000 Affy IDs to something around 20-15 000 ENSE IDs) which is the logic step, i end up with a list of around 77 000 IDs/genes. Does anyone has an idea what i am doing wrong?
Here is the code:
library(hgu133plus2hsenseprobe) library(hgu133plus2hsensecdf) CELs.start <- ReadAffy(celfile.path = "/Users/dimiter/genomark/NewTest/Working",cdfname="hgu133plus2hsensecdf") eset.rma <- rma(CELs.start) matrix <- exprs(eset.rma)
Thanks in advance!