it is the first time for me working with the Affy Human Exon St. 1.0. I followed the instructions of the 'oligo' package in Bioconductor - doing the RMA with 'core' parameter. Thus, I get an ExpressionSet and an expression matrix using exprs(exonCore).
Now I wanted to map the Affy Probe Ids using Biomart - so I got a lookup table, having all ids from the HuEx St.1.0 and e.g. RefSeq IDs.
When I do a simple lookup, only 1365 out of 22011 have RefSeq IDs.
1) What am I doing wrong? Why is that?
2) How is the best way to retrieve annotation?
3) My biologists want to see the expression of several genes - one value! Not only probe ids. What is the best way to do this?
Thank you very much in advance