[BioC] singlearrayerrormodel
w.huber at dkfz-heidelberg.de
w.huber at dkfz-heidelberg.de
Tue Nov 18 16:39:37 MET 2003
Hi Yeon-Ki,
I am not quite sure what sure what you mean by "single array error model"
but I suppose you mean error models for the individual intensities on a
spotted cDNA array rather than for their ratios or log-ratios.
There are some methods in the limma package for doing single-channel
normalization, I am not sure how much that is based on error models
(Gordon or Nathalie Thorne may be better in explaing this).
The package "vsn" allows to fit variance-stabilizing transformations,
which are closely related to error models. The error model used is the
two-component error model, i.e. an additive (constant) and a
multiplicative (proportional) error component.
Best wishes
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/abt0840/whuber
-------------------------------------
On Tue, 18 Nov 2003 kim750 at ggbio.com wrote:
> Hi! everyone,
> My name is Yeon-Ki Kim.
> Recently, single array error model seems to be prevalent in analyzing a
> microarray data. Does anyone give me some suggestions whether I can do
> this on Bioconductor or if so, how I can do it?
> Thanks.
> Yeon-Ki
Yeon-Ki Kim, Ph.D.
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