[BioC] pre-processing gene expression data from multiple Affymetrix chip types in one batch
Diana Hubbard
dhubbard at broadinstitute.org
Thu Oct 15 23:29:58 CEST 2009
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
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