[BioC] Affy and Custom CDF files

[Laurent Gautier]

On Sat, Mar 22, 2003 at 05:58:57PM -0500, Rafael A. Irizarry wrote:
> 
> 
> On Sat, 22 Mar 2003, Jeff Sorenson wrote:
> 
> > If I create a custom CDF file in which a particular probe may be listed in
> > more than one probe set, then will the results of the RMA algorithm in affy
> > still be valid?
> 
> i would think so. only small problem is that you will be counting these
> probes more than once in bg correction and normalization. if they are few
> shouldnt be a big deal.

There is an obvious workaround to that. Use the regular cdfenv for the
bg correction and normalization steps and use your own thing for the computation
of the summary values.


Hopin' it helps,



Laurent



> 
> good luck!
> 
> > 
> > Thanks,
> > Jeff Sorenson
> > 
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> >
> 
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