[BioC] Affy normalization with custom chip.
dmgatti at email.unc.edu
Mon Jun 4 20:34:54 CEST 2007
I'm analyzing a publicly available GEO data set (GEO5961) that uses a
custom array (GNF1M). The file download from GEO includes a .CDF file
for the array, CEL files and several other files that I'm not familiar with.
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Loading required package: tools
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Loading required package: affy
Loading required package: affyio
Loading required package: matchprobes
Loading required package: splines
> rawdata = ReadAffy("GSM138562.CEL", "GSM138563.CEL")
> norm = gcrma(rawdata)
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
Specified environment does not contain gnGNF1Musa
Library - package gngnf1musacdf not installed
Data for package affy did not contain gngnf1musacdf
Bioconductor - gngnf1musacdf not available
How can I load the GPL1073.CDF and GPL1073.probe files for the array
into the "environment" so that gcrma() can access them? I've tried
functions like getCDF(), but it's not clear how to specify a local file
as the source. And read.cdffile() reads into an object, but I'm not
clear how make that object visible to gcrma().
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