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@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@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > > Lana Schaffer > Research Specialist > The Scripps Research Institute > DNA Array Core Facility > >