[BioC] normalized probes

Lana Schaffer schaffer at scripps.edu
Tue Mar 4 20:07:24 CET 2008

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

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