Does vsn implement the 'maW' spot weights?
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Thomas S. Price
Post-doctoral researcher
Wellcome Trust Centre Telephone +44 1865 287608
for Human Genetics, Oxford www.well.ox.ac.uk/~tprice
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Hi Tom,
vsn does not use spot weights.
The purpose of vsn is not to make statements about individual genes,
but
only to calculate a normalization and data transformation per array
(or
per color channel). Typically, these are two parameters (an offset and
a
scale factor) per array. A few outliers or bad spots among the
thousands
will not make a difference, since vsn uses a robust estimation
procedure
that will ignore such outlying data points anyway.
Subsequent per-gene hypothesis tests or regression procedures may
benefit
from honoring spot weights, though.
Best regards
Wolfgang
-------------------------------------
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/mga/whuber
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On Wed, 24 Sep 2003, Tom Price wrote:
> Does vsn implement the 'maW' spot weights?
>
