[BioC] custom PM only chips and CDF files

[Celine Carret]

Hi Stephen,
I have been working with PM-only custom Affy chips for few years now and 
working with R has never been  a problem. You need to create a special 
environment or package using your CDF, and some of the affy function 
will not be available to you, but it isn't so much of a big deal.

Best wishes
Celine


Stephen Henderson wrote:

> 
>Hello
>I am interested to hear if anyone has had experience of using custom PM only chips (Affymetrix-for expression) together with Bioconductor? 
>
>In particular I'd like to know if there are any special arrangements needed for the CDF file (formatting changes etc) or if this works seemlessly with the affy Packages for instance?
>
>I don't foresee any problems but thought it would be prudent to ask on this forum to avoid unpleasant surprises.
>
>Stephen Henderson
>
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-- 
Celine Carret PhD
Pathogen Microarrays group
The Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK.
tel. +44 (0)1223 834 244 ext.7123
fax. +44 (0)1223 494 919
email: ckc at sanger.ac.uk
http://www.sanger.ac.uk/PostGenomics/PathogenArrays/