[BioC] custom PM only chips and CDF files

[Stephen Henderson]

Hi
That sounds fine-- and thanks for the re-assurance. When you say some
functions will not be available do you simply mean normalizations or
summaries using MM probes or other unforeseen consequences?


Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827


-----Original Message-----
From: Celine Carret [mailto:ckc at sanger.ac.uk] 
Sent: 06 December 2005 09:39
To: Stephen Henderson
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] custom PM only chips and CDF files

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/




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