[BioC] analyze HuEx array using HuGene .cdf file

[Jenny Drnevich]

See this post about removing individual probes or entire probesets 
from an Affy array:

https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html

HTH,
Jenny

At 04:01 PM 12/11/2008, shirley zhang wrote:
>Hi Larurent,
>
>Thanks for your quick reply.  You are right, CDF file also includes
>the location of probes on the chip. In that case, can I modify the
>HuEx .cdf file to mask those probes not found in Hugene array as
>NA/missing, and then use this modified .cdf file to analyze exon
>array? If can, do you know how to do it in R or other tools?
>
>Thanks a lot,
>Xiaoling
>
>
>
>
>On Thu, Dec 11, 2008 at 10:40 PM, Laurent Gautier <laurent at cbs.dtu.dk> wrote:
> > shirley zhang wrote:
> >>
> >> Dear List,
> >>
> >> I have a quick question. Since the HuGene probes are largely a subset
> >> of the HuEx probes, we would like to use that subset of probes for the
> >> HuEx array, then compare the results with that of using HuEx's own
> >> core probes which we already have. For this purpose,  can I use
> >> HuGen's .cdf file to analyze HuEx arrays?
> >
> > I'd say that you mostly likely can't.
> >
> > The CDF definition contains information relative to the relative spatial
> > location of the features (probes) on the chip, and unless the HuGene is a
> > subset also in the spatial sense of it (that is  "like HuEx but with probes
> > missing from their location on the array").
> >
> >> If not, how to
> >> generate/modify a .cdf file based on HuGen probes to analyze HuEx
> >> array data?
> >
> > HuGen(e{0,1}), HuEx, or else, you should have the corresponding .cdf
> > distributed with the arrays (and you'll contact Affymetrix if this is not
> > the case).
> >
> >
> > L.
> >
> >> Thanks,
> >> Shirley
> >>
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> >
> >
> >
> >
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu