[BioC] normalized probes

[Lana Schaffer]

Hi,
I am wondering if it is possible to obtain the 
normalized probe values after quantile normalization.
I have tried the option of using the destructive=F
and then looked at the intensity matrix and found the
values to be unchanged.  
I would like to know the different between the probe
matrix and the intensity matrix.  The index/order
has been changed in the probe matrix from the intensity
matrix and for my case the number of rows is reduced
for the probe matrix.
I will probably need to do the quantile normalization
separate from RMA to get the probe intensity values?

Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer at scripps.edu