[BioC] normalizaton between studies

[Anja.von.Heydebreck at merck.de]

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,
Anja

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