[BioC] Mismatch probe handling for exon arrays

[Steven McKinney]

The new Affy Exon chips do not have a mismatch probe for
every perfect match probe, but rather have a collection
of GC-varied background probes (about 50000 probes out
of the 6 million on the chip - the "background probe 
collection" BGP). 

Info is in, amongst others, 
http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf

Affy has modified their PLIER algorithm to use this
background probe collection to perform a "PM-GCBG"
correction, using the median BGP intensity for probes
with the same GC content as the PM probe.

Has any implementation of the PM-GCBG idea been done for
justRMA() or justPLIER() in R/BioC?

Can anyone comment on which input parameters or
control options of these functions should be specifically
set to allow these functions to do a reasonable job
of normalizing/correcting exon array data?  

For example, justPLIER() has argument usemm=TRUE
but no documentation about it - no doubt
usemm = FALSE is appropriate for the exon arrays.
But, will the algorithms still perform alright?

Are there newer versions of the algorithms that handle
the exon data configuration?

Any feedback appreciated.



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada