[BioC] Newbie. quantile normalization should be done on all conditions or within replicates of each condition?

James W. MacDonald jmacdon at uw.edu
Wed May 30 15:10:15 CEST 2012

You should normalize all conditions together, unless you have reason to 
suspect that the assumptions for a quantile normalization (most genes 
are not differentially expressed) does not hold.



On 5/30/2012 5:38 AM, Cytochalasin wrote:
> Hi all!
> Newbie here.
> I wondered wh ether quantile normalization should be done on an array
> containing all conditions of 1 experiment (eg containing both patients
> and healthy people) or within replicates of each condition (eg on data
> from patients and on data from healthy people separately)?
> Thanks indeed.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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