I'm trying to perform normalization on a set of Affy U133A chips. I'm using the affy library on R and was able to do the regular probeset level normalization using ReadAffy() and rma() on the affybatch object.
But now I want to do the same thing but for the probe level data. The problem is, I cannot use expresso with summarization disabled (a summary argument has to be provided or it returns an error). Nor can I use the function pm() because the probe to probeset id numbers are lost. That is, with pm() the row identifiers turn into probe numbers. but with the function probes() i still get 1007_s_at1, 1007_s_at2, etc.
Is there a way I can do all the steps that RMA does to the probe level data, without summarization, and with keeping the associated probeset id information to each probe?
I hope this was was clear. If not, I can elaborate.