[BioC] RMA with biological replicates

Dipl.-Ing. Johannes Rainer johannes.rainer at tugraz.at
Thu Jul 29 16:13:36 CEST 2004

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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