[BioC] gcrma

[Zhijin Wu]

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
> 
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