[BioC] Affy normalization with custom chip.

Daniel Gatti 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.

 > library(gcrma)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

     Vignettes contain introductory material. To view, type
     'openVignette()' or start with 'help(Biobase)'. For details
     on reading vignettes, see the openVignette help page.

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().

Dan Gatti

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