[BioC] normalization across sites

[Sean Davis]

Weiwei Shi wrote:
> Hi,
>
> Suppose that I have two sets of arrays, both of which use the same
> platform. My question is, if I have datasets which have been
> preprocessed, what's the best way for me to normalize them. Currently
> I just scale them sample-wise; but not sure of it.
>
> Otherwise, should I go back to .CEL file? But how to proceed from there?
>   
Start from raw data, yes.  You may need to use an ANOVA or linear model 
to deal with confounding variables.  Quality control is especially 
important.

Sean