[BioC] Affymetrix MAS5 Calls

[Paul Boutros]

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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