[BioC] gcrma

[Lana Schaffer]

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