[BioC] Summarize with RMA using Alternative CDF

[Arteaga Salas, Jose M]

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.