[BioC] Tiling array application

[Shinhan Shiu]

Hi Fangxin,

Thanks a lot for the message. I see what you are saying then. I am trying 
to look up the paper but can't find it. Wu has published a comment in 
Nature Biotech:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15175677

Which talk about a paper "A model of molecular interactions on short 
oligonucleotide microarrays" by Zhang et al.:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12794640

Are these the papers you talk about. Thanks!

Shinhan

At 12:43 PM 4/4/2005, you wrote:
>Hi Shinhan;
>In GCRMA, bg.adjust.affinities use PM and MM intentisities to fit a model
>to extract the signal ( what we call background correction). This step
>used sequence information for affinity calculation. Without MM
>intensities, the model is not complete or there is no model at all,
>meaning this step is meaningless.  So if I understand correctly, it is
>impossible to adjust affinities for PM probes without MM information.
>
>For details, reference paper: "A model based background adjustment for
>oligonucleotide expression arrays" by Zhijin Wu etc.
>
>Fangxin
>
>
>
> > 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
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor at stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >
> >> >
> >> >
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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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> >
>
>
>--
>Fangxin Hong, Ph.D.
>Plant Biology Laboratory
>The Salk Institute
>10010 N. Torrey Pines Rd.
>La Jolla, CA 92037
>E-mail: fhong at salk.edu

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