x.rma <- rma(raw.data)
http://ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040006#article1.body1.sec5.sec1.sec1.p5

Hi,

with R 2.15, this command was not working for me with mouse exon array. I succeeded in loading and normalizing the data with the following lines of code. I though it may be usefull to know for someone who would experience the same problem :

phenoData = read.AnnotatedDataFrame("pheno.csv")

raw.data = ReadAffy(filenames=phenoData@data$FileName,
phenoData=phenoData,
verbose=T,cdfname="mouseexonpmcdf")

phenoData contains the same things as the covdesc file described in the article. Loadinf and PreProcessing are done in one single step (replacing lines 2, 3 and 4).