[BioC] Normalizing after MAS 5.0

[Michal Blazejczyk]

Hello group,

According to the Bioconductor Help for function expresso():

  "For the mas 5.0 and 4.0 methods ones need to normalize after
   obtaining expression. The function affy.scalevalue.exprSet
   does this."

What does it really mean, "for the mas 5.0 method" in this case?
When calling expresso, "mas" can be set as a method for background
correction, PM correction, and probe summarization.  In which of
these cases should the custom normalization (affy.scalevalue.exprSet)
be used?

Best regards,

Michal Blazejczyk
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
http://genomequebec.mcgill.ca/FlexArray