[BioC] using MM

[Rafael A. Irizarry]

hi all,

sometime ago someone asked about thoughts related to the use of mismatch
probes (MMs) in affy arrays. The developmental package gcrma provides
an implementation of a version
of RMA that uses MMs. It also uses sequence information. the new method
appears to improve the performance of RMA in terms of accuracy (estimated
fold changes are bigger). the method is described here:

http://www.biostat.jhsph.edu/~ririzarr/papers/gcpaper.pdf

the code (which is very slow) is still under development thus feedback is 
greatly appreciated. 

cheers,
rafael