[BioC] Replace method, AffyBatch, pm or mm

[Laurent Gautier]

laurent buffat wrote:
> 

<...cut...>

> Instead of "pm(aBatch, aProSetName)" to get or replace intensity of probes
> of a probeset in a affybatch, I have to use Intensity & probesIndex :
> 

Good.
As a general comment, when going to tweaks and 'non-mainstream' 
manipulations with 'affy', I would recommend to leave wrappers alone and 
use more 'primitive' functions. A lot of the package was designed with 
that in mind: primitive (but convenient) functions, and wrappers for 
some common operations (for example, 'expresso' is a wrapper around 
individual pre-processing operations for example, and the pre-processing 
operations are themselves wrappers around pre-preprocessing core 
functions operating on matrices of data... same idea with pm vs. 
indexProbes + intensity).



L.