[BioC] Tiling array application

[Zhijin Wu]

To estimate non-specific binding, some negative control probes are
desired. However, arrays do not have to have the MM probes as in
Affymetrix GeneChip design (one for each PM probe) as negative control
probes. They simply should be probes that do not match any specific target
in your sample.
  The function bg.parameters.ns estimates the relationship between probe
affinities and non-specific binding(NSB) with one set of negative control 
probes (in Affy chips, the MMs), and predicts NSB in another set of probes
(in Affy chips, the PMs). So as long as you have some negative controls,
you can modify the parameters passed to "bg.parameters.ns" accordingly. If
you have no negative control probes at all, you probably need some
extra assumption, otherwise the NSB and SB may not be identified. If you
can assume a large proportion of specific target to be absent, you can
also simply pass PM affinities and PM intensities instead of the MMs to
bg.parameters.ns().


> 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
> > >> >
> > >> >
> > >> >
> > >> > **********************************************************
> > >> > Electronic Mail is not secure, may not be read every day, and should
> > >> not be used for urgent or sensitive issues.
> > >> >
> > >> > _______________________________________________
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> > >> > Bioconductor at stat.math.ethz.ch
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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
> 
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