Hi, Regarding the discussion of the rma background correction: If it doesn't use the MM values to estimate bg anymore, what is the background correction 'rma' in expresso actually doing? Many Thanks, Cass. ------------------------------------------------- This mail sent through UCL Biochemistry's Webmail: http://webmail.biochem.ucl.ac.uk/ (unsecured) https://webmail.biochem.ucl.ac.uk/ (secured)

you can read the reference below for some details or look at the code for all the details: "bg.correct.rma" http://stat-www.berkeley.edu/users/bolstad/stuff/BAUGM.pdf has a bit more than the reference. a quick summary: it uses the PM distribution to get an overall background level. then a transformation based, on a background nosie + signal model is used. Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics. Vol. 4, Number 2: 249-264. On Wed, 25 Jun 2003 johnston@pat.biochem.ucl.ac.uk wrote: > Hi, > > Regarding the discussion of the rma background correction: If it doesn't use > the MM values to estimate bg anymore, what is the background correction 'rma' > in expresso actually doing? > > Many Thanks, > > Cass. > > ------------------------------------------------- > This mail sent through UCL Biochemistry's Webmail: > http://webmail.biochem.ucl.ac.uk/ (unsecured) > https://webmail.biochem.ucl.ac.uk/ (secured) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >