[BioC] RMA with biological replicates

[Adaikalavan Ramasamy]

Perhaps. But my main concern with performing RMA on patient by patient
is that the difference between patients could possibly be confounded
with normalisation. i.e. You cannot tell if an observed difference is
due to patient difference or due to normalisation.

The other problem with doing that is that you only have 3 chips. The
following thread is almost a year old but it indicates possible problems
with only 3 chips.
 http://files.protsuggest.org/biocond/html/3346.html

Regards, Adai.

On Thu, 2004-07-29 at 15:13, Dipl.-Ing. Johannes Rainer wrote:
> ok,
> normalizing all together because of the better model parameter fitting?
> 
> 
> 
> Quoting Stephen Henderson <s.henderson at ucl.ac.uk>:
> 
> >  all together.
> >
> > -----Original Message-----
> > From: Dipl.-Ing. Johannes Rainer
> > To: bioconductor at stat.math.ethz.ch
> > Sent: 7/29/04 2:22 PM
> > Subject: [BioC] RMA with biological replicates
> >
> > hi,
> >
> > i have again a question about RMA and how it works with a different
> > number of
> > chips.
> > we are looking at the response of patients to a specific treatment, so
> > we got
> > biological replicates and no technical ones (as we have not enough
> > material
> > from the patients). at the moment i got 9 chips, 3 patients, 3 time
> > points for
> > each patient.
> > What is now the best way to normalize them? normalize them all together
> > with
> > RMA, or normalize the chips from each patient separatly (that means
> > normalize
> > the 3 chips from patient one together, then those from patient 2...)?
> > As i think, RMA gives better results if i have more chips to normalize
> > together
> > (more chips with roughly the same expression result in better fitted
> > model
> > parameters i guess).
> > has anyone a conclusion what's the best was?
> >
> > thanks, jo
> >
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