[BioC] Creating a Custom CDF Environment

James W. MacDonald jmacdon at med.umich.edu
Thu Jun 8 17:32:42 CEST 2006

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.



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

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