I'm working with an Affymetrix rat transcriptome in R and would like to compare, say, expression levels of MAOA and MAOA versus a housekeeping gene like ACTB. I've gone through the basic initial stages:
rawdata = ReadAffy() eset = rma(rawdata)
and am aware of the affy and limma packages but not entirely sure how to go about specifying only two or three genes for analysis/comparison. Help?