[BioC] normalizaton between studies

Anja.von.Heydebreck at merck.de Anja.von.Heydebreck at merck.de
Fri Dec 10 14:41:16 CET 2004

Dear Arne,

> The problem is that the studies have quite different intensity
> distributions of the PMs). I've some doubts that RMA or VSN are
> appropiate normalization methods for this problem. Forcing all
> distributions to be the same may buffer the very strong study
> effect but may also erase some of the tiny (but significant)
> differences due to dose.

Actually, VSN does not enforce intensity distributions to be the
same. The normalization in VSN amounts to an affine-linear mapping
of the intensities of each chip, that is, for each chip only a
multiplicative/scaling factor and an additive offset are estimated
from the data.

Best regards,

Dr. Anja von Heydebreck
Global Technologies
Bio- and Chemoinformatics
Merck KGaA
64271 Darmstadt
Phone: +49-6151-723235, Fax: +49-6151-723329
Email: anja.von.heydebreck at merck.de

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