[BioC] Affymetrix Normalization based on the controls?

[Khan, Sohail]

Dear List,

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 (normalizing to doped-in RNAs?), etc. Thanks.

 


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