[BioC] affybatch object too big

[Noemi Andor]

Hi,

I have a problem with the loading of an affybatch object from cel-files. I have multiple cel files and want to analyze them all together, yet the amount of data is to big to be loaded. I am interested only in a subset of genes within those cel-files. So I could load the cel-files into 3 or 4 affy objects, then read the expression values of the genes of interest and merge them again. But if I read them separatly, the background correction wil not be global, and I do not know how to read them without background correction:

pd=read.AnnotatedDataFrame("BI_samples_1.txt", header=TRUE, row.names=1)
a= ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE)
eset<-rma(a)
e206123_at<-exprs(eset["206123_at"])
...
e210684_s_at<-exprs(eset["210684_s_at"])
e1<-rbind(e206123_at,..., e210684_s_at)

If I do the same for BI_samples_2.txt the corresponding e2 will not be comparable to e1, am I right?

Would be very greatfull for a good solution to my problem?

best regards,

Noemi