[BioC] normalize by or across all treatments

[Isaac Neuhaus]

Leanna House wrote:

>In replicates of 3, I have a set of control and 4 treatment arrays.  My
>question is, do I normalize (via rma) using all of the arrays at once, or
>do I normalize by treatment.  I have asked other reliable sources and have
>received conflicting responses.  I feel the issue is that, in one case, I
>may, if not completely wipe out, severely diminish any possible treatment
>effects, whereas, in the other case, I may actually induce a treatment
>effect.  Any thoughts?
>  
>
I normalize across all experiments (and using RMA) despite the fact as 
you mentioned you  may reduce any treatment effect. My only suggestion 
(which could be already too late) is to design the experiment in such a 
way that you can utilize two-way ANOVA with random block effect. What is 
your experimental design?

I

>Thank you so much,
>Leanna
>
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