[BioC] Normalization of Affymetrix data using the house keeping controls.

[Khan, Sohail]

Dear List,

There was no response to my previous post (see below).  Is this not an appropriate question for this??  

I have a data set from Affymetrix experiments where the assumption of "few changes" between control and experimental samples may not hold, so global normalization may be inappropriate.  I'm unsure what normalization method is best (house keeping genes?), etc. Thanks.


Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076