[BioC] RMA with biological replicates

[Dipl.-Ing. Johannes Rainer]

that's ok, but i am afraid that these 3 biological replicates differ to much
(three different patients), so that i loose some information when normalizing
them all togehter. i think also that the best way to normalize them is to
normalizing them all together with RMA.
what replicates are you using? technical or biological? you are analyzing 2
replicates exposed to 6 different treatments?


Quoting Naomi Altman <naomi at stat.psu.edu>:

> There may be problems with only 3 arrays.  But there should not be a
> problem with 3 replicates for 3 times = 9 arrays.  We used RMA on 2
> replicates for 6 treatments = 12 arrays, and the results seemed fine.
>
> --Naomi
>
> At 03:28 PM 7/29/2004 +0100, Adaikalavan Ramasamy wrote:
> >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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> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
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