[BioC] Tiling array application

[Shinhan Shiu]

I should have been more specific. What I want to do is to use the affinity 
calculated by gcrma to account for GC contents of the probes. So I am 
not  planning to use the rma part of GCRMA.

gcrma first calls compute.affinities to generate affinity for each probe. 
After optical correction (bg.adjust.optical), gcrma calls gcrma.engine 
which calls bg.adjust.affinities. This is the method I am interested in. I 
was hoping to use this method to correct the raw intensity for probe GC 
contents.

But I found that bg.adjust.affinities calls bg.parameters.ns that requires 
MM probe intensity, MM probe affinity, and PM probe affinities. I am a bit 
surprised because, as James commented, I thought gcrma don't need MM 
information.

What I would like to find out is: how I should pass the parameter or modify 
the method for adjusting affinities for PM probes without MM information.

Shinhan

At 01:09 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

********************************
  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago