[BioC] gcrma

[Zhijin Wu]

I will add it to the affycomp list soon. You can submit it to the affycomp
page as well. 
affycomp.biostat.jhsph.edu/


On Thu, 6 Jan 2005, Lana Schaffer wrote:

> Do you have any benchmarks for theses options?  Are they in your
> published papers?
> Thanks,
> Lana Schaffer
> 
> 
> >===== Original Message From Zhijin Wu <zwu at jhsph.edu> =====
> >The "fullmodel" option uses both MM intensities and PM probe sequences;
> >The  "affinities" option uses MM probes only as negative control probes to
> >estimate the relationship of NSB with sequence. IT does not use the MMs as
> >paried measurement of background for each PM probe. The idea here is that
> >a set of "non-PM" probes are needed but not one for each PM.
> >The "MM" option uses only the MM measurements for background adjustment.
> >
> >
> >On Wed, 5 Jan 2005, Lana Schaffer wrote:
> >
> >> Hi,
> >> I have been reading the papers "A Model Based Background Adjustment for
> >> Oligonucleotide Expression Arrays" and "Stochastic Models Inspired by
> >> Hybridization theory for short Oligonucleotide Arrays" and comparing
> >> these papers to the options available in Bioconductor for gcrma.
> >> I request some clarification for the options: fullmodel, affinities,
> >> mm, and constant.  Does the fullmodel use the MLE or the Bayes estimate?  
> Is
> >> there some literature that compares the results of the various options to 
> one
> >> another, since the options don't seem to be exactly those presented in the
> >> papers?  I assume the mm option to use an unadjusted mm?
> >> So would you say that gcrma still uses the mm's?
> >> Thanks for your input.
> >> Lana
> >>
> >> Lana Schaffer
> >> Research Specialist
> >> The Scripps Research Institute
> >> DNA Array Core Facility
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
> 
> Lana Schaffer
> Research Specialist
> The Scripps Research Institute
> DNA Array Core Facility
> 
>