I think these are exon arrays (based on cdfname="hugene10stv1") for which you'll need to use the oligo package, not affy. http://www.bioconductor.org/packages/release/bioc/html/oligo.html On 09/09/2013 10:14, "Gundala Viswanath" <gundalav at="" gmail.com=""> wrote: >I have an Affymetrix CEL files downloadable here (31.7MB): > >http://hugefiles.net/4fqnokdo9irv > >What I want to do is to perform an RMA analysis using affy package. >This is the code > >__BEGIN__ >#!/usr/bin/Rscript >#install the core bioconductor packages, if not already installed >source("http://bioconductor.org/biocLite.R") >biocLite("affy") > >library(affy) ># After unzipping the tmp_cel.zip file >cels=list.files("/Users/gundalav/Desktop/tmp_cel/",pattern="CEL") > ># Set working directory >setwd("/Users/gundalav/Desktop/tmp_cel/") > ># Read CEL file >raw.data1=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hugene10stv1") > ># Perform RMA normalization. It breaks here >data.rma.norm=rma(raw.data1) >__END__ > >The error message I got was > >Error in .local(object, ...) : subscript out of bounds > >What's the way to address that? > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor