[REMAPPING OF PROBES] Remapping libraries installed mogene10stv1mmensecdf mogene10stv1mmenseprobe mogene10stv1mmensgcdf mogene10stv1mmensgprobe remapping packages for R were downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF Go to the U Michigan BrainArray site: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp Choose the newest verison Click on your preferred reference gene set (like Entrez Gene): http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/entrezg.asp Choose your array design (like HGU133Plus2), and choose the "C" link for your platform (like Windows) http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/entrezg.download/hgu133plus2hsentrezgcdf_12.1.0.zip If you want to use GCRMA, you also need the package from the "P" (probe) link. Install the package(s). in R: do install.packages("location of the gz file",repos=NULL,type="source") May need to install AnnotationDbi as well: to do so, in R: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") Use your usual R code but just modify it like this: # Use this new library library(hgu133plus2hsentrezgcdf) # GCRMA also requires this probe information # library(hgu133plus2hsentrezgprobe) # Go to the CEL file directory and specify the custom CDF with the ReadAffy command CELs.entrezgene = ReadAffy(cdfname="hgu133plus2hsentrezgcdf") # And then process as usual, like eset.entrezgene = rma(CELs.entrezgene) # Otherwise, for RMA, we can use the justRMA commmand, without creating an AffyBatch object eset.entrezgene = justRMA(cdfname="hgu133plus2hsentrezgcdf") Interpretation: For custom CDFs keyed to Entrez Gene IDs, a probeset like 10000_at represents Entrez Gene with ID = 10000 (AKT3) For other types of transcriptomes, also remove the "_at" to get the gene/transcript ID. ###download ens table from biomart, and convert cuta.py -f2,1 ens.biomart.table.txt > ens.biomart.table.ensID2GeneName