[BioC] Tiling array application
Shinhan Shiu
shiu at uchicago.edu
Mon Apr 4 23:41:38 CEST 2005
Hi Zhijin,
Thanks for the message. I have a question on the second solution: passing
only the PM intensity and PM affinity information to bg.parameter.ns. You
mentioned that the assumption in excluding MM information is when "a large
proportion of specific targets are absent". I wonder if you can clarify
this a little. Do you mean that "the intensities of a large proportion of
the probes are simply background"? Also, do you have some estimate as to
how large a proportion is sufficient?
Also, does this approach (excluding MM info) lead to a higher false
negative rate when comparing to using negative controls for MM? Thanks again.
Shinhan
At 01:18 PM 4/4/2005, you wrote:
>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.
> > > >> >
> > > >> > _______________________________________________
> > > >> > Bioconductor mailing list
> > > >> > 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
********************************
Shinhan Shiu
Dept. of Ecology and Evolution
University of Chicago
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