[BioC] RMA with biological replicates

[Naomi Altman]

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
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > >
> > >
> > > **********************************************************************
> > > This email and any files transmitted with it are confidential and
> > > intended solely for the use of the individual or entity to whom they
> > > are addressed. If you have received this email in error please notify
> > > the system manager (it.support at wibr.ucl.ac.uk). All files are scanned for
> > > viruses.
> > > **********************************************************************
> > >
> > >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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)
University Park, PA 16802-2111