[BioC] pre-processing gene expression data from multiple Affymetrix chip types in one batch

[Diana Hubbard]

Hi,

I would like to know how to pre-process gene expression data (CEL files) 
from the Affymetrix chip types Hgu_133A and Hgu_133A2.0 concurrently in 
one AffyBatch using the current version of R and  would like to do it in 
a gene centric way, not by probe set.  I have been doing it using the 
following code, in R2.4:


x1<-ReadAffy(celfile.path="path1")
x2<-ReadAffy(celfile.path="path2")
res<-combineAffyBatch(list(x1,x2), c("hgu133plus2probe", 
"hgu133aprobe"), newcdf="comb", verbose=TRUE)
comb<-res$cdf
x<-rma(res$dat)
x.exprs<-exprs(x)
write.table(x.exprs, file="results.txt", sep="\t")

but this depends on several Bioconductor packages from Bioconductor 1.9 
that are not supported anymore, and this only returns expression data by 
probe set.   I have gene centric cdf files for R2.9, so being able to 
pre-process the data in one batch using these cdf files would be great.

Thanks a lot,
Diana