[BioC] Creating a Custom CDF Environment

[James W. MacDonald]

Hi Martin,

martin doherty wrote:
> Hi,
> 
> I know this has been asked many times, but I've read all the groups
> and literature available. I have a custom CDF that isn't available from
> BioConductor, initially I tried to install it as a package but I couldn't
> install the sofrware on my machine, and was unalbe to access a UNIX
> machine.
> 
> So now all I wish to do is create a CDF environment from which I can
> do my analysis. This is what I do:
> 
> *R> cleancdfname("ADXCRCG2a520319.CDF")*
> *     [1]  "adxcrcg2a520319.cdf"*
> **
> *R> adxcrcg2a520319cdf = make.cdf.env("ADXCRCG2a520319.CDF")*
> *     Reading CDF file.*
> *     Creating CDF environment*
> *     Wait for 615 dots............*
> *R>Data <- ReadAffy()*
> *R>deg <- AffyRNAdeg(Data)*
> *    Error in getCdfInfo(object) : Could not obtain CDF environment,
> problems encountered:
>     Specified environment does not contain ADXCRCG2a520319

Name your environment ADXCRCG2a520319 instead of adxcrcg2a520319cdf and 
it should work.

Best,

Jim



-- 
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


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