[BioC] Summarize with RMA using Alternative CDF

Henrik Bengtsson hb at stat.berkeley.edu
Fri Jan 23 16:56:38 CET 2009

A CDF (chip definition/description file) is an Affymetrix CDF file
(one file/no directory).  In Bioconductor there are CDF packages also
known as/that contains CDF environments.  CDF packages can be created
from CDF files.  You need a CDF *package* - a CDF *file* will not
work.  So, argument 'cdfname' takes a package name.  You are not the
first one making this mistake.

See also the aroma.affymetrix package which works with CDF files
(including custom ones) directly.  It can reproduce the results of
both affy and affyPLM near perfectly.



On Fri, Jan 23, 2009 at 5:32 AM, Arteaga Salas, Jose M
<jmarte at essex.ac.uk> wrote:
> Dear List,
> I am running an experiment with some HG-U133A arrays.
> I identified some dodgy probes, and I have created an alternative CDF
> file without these probes.
> Now, I want to summarize my .CEL files with either rma() or just.rma()
> to analyze the impact of my dodgy probes in gene expression.
> I am trying to run these commands, and then obtaining this error:
>> data=ReadAffy(cdfname="MyAlternativeCdf.CDF");
>> rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF ");
> Error in getCdfInfo(object) :
>  Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MyAlternativeCdf.CDF
> Library - package MyAlternativeCdf.cdf not installed
> Bioconductor - MyAlternativeCdf.cdf not available
> My guess so far is that I am getting this error because of the C
> implementation of RMA, that I don't seem to have available in any folder
> of my "affy" package instalation.
> Is there anyway that I can get around this problem?
> Thank you for your kind replies.
> Jose Manuel Arteaga
> PhD Student in Statistics
> University of Essex, U.K.
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