[BioC] problem with vsn and affy data...

[Wolfgang Huber]

Hi Stephen,
vsn is another package on bioconductor.org that estimates for each array a
normalization factor and an offset. It then performs a (kind of) log-linear
hybrid transformation of the data such that the resulting differences are
"log-ratios" with a constant variance along the whole intensity range.
Equivalently, you can consider them z-scores of log-ratios, i.e. raw
log-ratios divided by their variance. See below web site (Publications) for
more details.

The method can be applied to both cDNA and affy probe intensities, hence
it's a separate package. It can be added to the normalize.AffyBatch.methods
list through the mechanism described in the affy documentation, or also in
the vsn vignette. The implementation is somewhat slow at this point.

Best regards -
Wolfgang Huber

Division of Molecular Genome Analysis (Dep. Poustka)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 580
69120 Heidelberg, Germany

w.huber@dkfz.de
http://www.dkfz.de/abt0840/whuber
Tel +49-6221-424709
Fax +49-6221-42524709


-----Original Message-----
From: Stephen Henderson [mailto:s.henderson@ucl.ac.uk]
Sent: Wednesday, December 18, 2002 5:06 PM
To: 'Wolfgang Huber'; Oliver Hartmann; bioconductor
Subject: RE: [BioC] problem with vsn and affy data...


Sorry.

What is the vsn method you're talking about? I don't see this in my
normalize.AffyBatch.methods

Stephen Henderson