Hi,

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!

You haven't done anything wrong, except perhaps for being confused as to what ENSE means. Please note that ENSE is Ensembl Exon IDs, whereas ENSG is Ensembl Gene IDs. So if you want to summarize at the gene level, based on Ensembl genes, then you need the hgu133plus2hsensgcdf, which has 20,049 genes as compared to the ENSE version, which has 77,898 exons.