[BioC] gcrma with bpmap file instead of cdf file

Baoqiang Cao caobg at email.uc.edu
Thu Jan 11 17:44:54 CET 2007

Hi Julia,

I went through the metadata website and couldn't find it. 
Here is what I got after gcrma:
> tmp<-ReadAffy("sample.cel")
> gcrma(tmp)
Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered:
Specified environment does not contain Chrom21-22A_2um
Library - package chrom2122a2umcdf not installed
Data for package affy did not contain chrom2122a2umcdf
Bioconductor - chrom2122a2umcdf not available

I couldn't find the "chrom2122a2umcdf". Any help will be highly appreciated!


---- Original message ----
>Date: Thu, 11 Jan 2007 10:54:56 +0100
>From: Julia Engelmann <julia.engelmann at biozentrum.uni-wuerzburg.de>  
>Subject: Re: [BioC] gcrma with bpmap file instead of cdf file  
>To: caobg at email.uc.edu, bioconductor at stat.math.ethz.ch
>Hi Baoqiang,
>have you looked for the cdf-file of your chiptype in the Metadata
>section of the Bioconductor website?
>Baoqiang Cao wrote:
>> Dear All,
>> I'm trying to use gcrma to analysis the data I have. Unfortunately, I only have cel file and the bpmap file for the arrays. It seems that cdf file is manditory for gcrma, any possibile way I could bypassing it with the bpmap file? Any help will be certainly appreciated.
>> Best,
>>  Baoqiang Cao
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