[BioC] Tiling array application

[Naomi Altman]

To continue this thought, rma has 2 steps:

probe normalization
probe set compilation

For a tiling array, it seems like probe normalization probably makes sense 
(and quantile normalization would be the simplest choice).

Since there are probe sets, the 2nd set is meaningless.

--Naomi

At 02:09 AM 4/2/2005, Kasper Daniel Hansen wrote:
>On Fri, Apr 01, 2005 at 08:04:28PM -0500, James MacDonald wrote:
> > It doesn't make any sense to use gcrma() if you don't have MM probes;
> > the idea behind gcrma is to come up with a better measure of background
> > than the MM measure itself. A modification of gcrma() that doesn't use
> > MM probes is rma().
>
>And if you are using a tiling array it does not seem to make sense (to
>me at least) to use rma, since tiling arrays does not have the cpncept
>of probesets.
>
>But I do not know your particular array, so I may be wrong.
>
>Kasper
>
> > >>> Shinhan Shiu <shiu at uchicago.edu> 04/01/05 5:13 PM >>>
> > We are trying to use GCRMA to adjust raw intensity values from tiling
> > chip
> > experiments (Arabidopsis). But the affy Arabidopsis tiling chip do not
> > have
> > mismatch probes and it seems the mismatch probe intensity is absolutely
> > required in:
> >
> > bg.parameters.ns
> >
> > Where the mismatch probe intensities, mismatch probe affinity, and
> > perfect
> > match probe affinities are passed. I wonder how this function can be
> > modified so only perfect match probe info is used. Thanks.
> >
> > Shinhan
> >
> >
> > ********************************
> >   Shinhan Shiu
> >   Dept. of Ecology and Evolution
> >   University of Chicago
> >
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>--
>Kasper Daniel Hansen, Research Assistant
>Department of Biostatistics, University of Copenhagen
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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