[BioC] RMA: Affy MoEx and background correction

[Peter Saffrey]

I am using the affy library to compute RMA values on mouse exon arrays, 
using the mouseexonpmcdf from here:

http://xmap.picr.man.ac.uk/download#mmcdf

It works fine, but I wanted to check some of the details of the 
implementation and hoped somebody on this list could help.

As I understand it, the background correction step of the RMA 
calculation usually works on the mismatch (MM) probes on the array. 
However, on the exon array, there are no MM probes, so the calculation 
is done based on a separate pool of background probes. There is a 
description here:

http://media.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf

Is this seamlessly happening behind the scenes when I run RMA with the 
mouse exon CDF or do I need to do something else to ensure the proper 
background correction is taking place?

Peter