On Fri, Jan 23, 2009 at 8:32 AM, Arteaga Salas, Jose M
<jmarte@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?
>

Actually, the problem is that you need to build a cdf environment.  The cdf
file is not directly useful for bioconductor.  The package makecdfenv will
do this for you.  Just work through the vignette.

Hope that helps.

Sean

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