[BioC] Supported CDF libraries

[James W. MacDonald]

Hi Andy,

Andy Reynolds wrote:
> Hi,
> I'm trying to use the affyQCReport package to assess the quality of some
> Affymetrix arrays, however; I'm apparently using an unsupported CDF library
> file.  I've tried to create a new cdf environment with the makecdfenv
> package with no success.  The code snippets for both attempts are as below.
> Can anyone offer any insights into either of these problems?
> 
> Thanks in advance.
> Andy
> 
> 
>> affyBatch <- ReadAffy()
>> QCReport(affyBatch,file="AffyQC.pdf")
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered:
> Specified environment does not contain DogSty06m520431
> Library - package dogsty06m520431cdf not installed
> Data for package affy did not contain dogsty06m520431cdf
> Bioconductor - dogsty06m520431cdf not available
> 
> 
> 
> make.cdf.package("DogSty06m520431.cdf", species = "Dog")
> Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress,  :
> 
>         makecdfenv does not currently know how to handle cdf files of this
> type (genotyping).

This is the only problem you need to address. As far as makecdfenv is 
concerned, the chips you have are SNP chips, not expression chips (and 
affy/makcdfenv are only designed to handle expression chips). Given the 
'sty' in the chip name, I would imagine makecdfenv is correct in this 
regard.

To analyze SNP chips you will need to use the oligo package, and build 
the pdInfo package using the pdInfoBuilder package. To date I think the 
only SNP chips that have been processed using either of these packages 
were Human, so there may be some snags that you will have to overcome.

Best,

Jim



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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623