[BioC] vsn add-on normalization

Markus Schmidberger schmidb at ibe.med.uni-muenchen.de
Thu Mar 19 13:05:35 CET 2009


I have a question for the vsn normalization towards a reference data set.
(my real data are much more)

I will normalize 5 Arrays with vsn:
ab_ref <- ReadAffy(filenames=celfiles[1:5])
fit_ref <- vsn2(ab_ref)

After this I can add 2 Arrays  with normalization towards a reference:
ab_add <- ReadAffy(filenames=celfiles[6:7])
eSet1 <- vsnrma(ab_add, reference=fit_ref)

And than I would like to add two more Arrays:
ab_add2 <- ReadAffy(filenames=celfiles[7:8])
eSet2 <- vsnrma(ab_add2, reference=fit_ref)

Do I use the old reference (fit_ref) for the second add-on normalization 
or the fit from the first add-on normalization or a combination of the 
first two fits?


Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://www.ibe.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4497

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