[BioC] Normalization with common reference

Wolfgang Huber w.huber at dkfz-heidelberg.de
Thu May 27 20:09:11 CEST 2004

Hi Emanuele,

first a naughty question: why did you choose this experimental design 
(gDNA as a reference) if you didn't have a plan for how to proceed with 
the data?

One thing you could try is to simply forget about the reference and
essentially treat the arrays as if they were single-color. There are a
number of single-color normalization methods, including vsn (package
vsn) and quantiles normalization (package affy). You could still use the
reference channel for spot QC.

But I would also be interested to see if anyone had an idea for how to
more gainfully employ the reference channel.


marchiem at libero.it wrote:
> Deal All,
> I would like to know if there is in BioC a normalization method suitable for arrays where RNA samples are hybridazed with genomic DNA as common reference.
> the channel with the gDNA would be always constant and strong for every spot and of course we cannot apply any method that assumes an average equal expression level for both channels...
> what do you reckon?
> thank you very much in advance.
> Best regards.
> Emanuele
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Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber

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