[BioC] RMA normalization for Affymetrix CEL Files (Subscript out of bounds error)

[Sidders, Benjamin]

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?
>
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