[BioC] normalization across sites

Weiwei Shi helprhelp at gmail.com
Fri Jun 22 03:51:52 CEST 2007

Ok, if I understand correctly, I should combine two sources of data
and run RMA on it?

On 6/21/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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

Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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