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

[James W. MacDonald]

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.

Best,

Jim



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.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099