pre-processing gene expression data from multiple Affymetrix chip types in one batch
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@diana-hubbard-3734
Last seen 9.6 years ago
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
cdf probe cdf probe • 590 views
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