[BioC] Affymetrix MAS5 Calls

Rafael A. Irizarry ririzarr at jhsph.edu
Sun Aug 3 22:50:07 MEST 2003

you can use the method probeset to extract the pms and mms from instance
of AffyBatch. you should be able to code the algorithms described in the
affy manual. 

On Fri, 1 Aug 2003, Paul Boutros wrote:

> Hi all,
> Just wondering if there was some way to replicate the expression-level calls in 
> MAS5 here?  I'm primarily interested in the calls made for each array: is a 
> particular ProbeSet present, absent, etc.
> I would like to be able to compare the results of those calls between RMA, 
> MBEI, and MAS5 flavours of normalization, BG-correction, and MM-correction.  My 
> understanding is that these are the only factors differing between the three 
> methods for the purpose of "expression calls" (summary method is irrelevant).
> I realize that this isn't trivial because MAS5 "perturbs" the bg-factor before 
> doing the rank-test, so there isn't a direct analogue to RMA or MBEI.  Any 
> suggestions on this are very much appreciated.
> Paul
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