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

Gundala Viswanath gundalav at gmail.com
Mon Sep 9 11:14:24 CEST 2013


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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