[BioC] Linear and spline normalization

Johannes Freudenberg mai98ftu at studserv.uni-leipzig.de
Tue Sep 30 11:46:36 MEST 2003


you can type

> normalize.methods(affybatch.example)

to get all the normalization methods implemented in BioConductor:

[1] "constant"         "contrasts"        "invariantset"     "loess"           
[5] "qspline"          "quantiles"        "quantiles.robust"

The constant method does what Schadt et al. call linear normalization. It takes 
an argument called FUN with default = mean. You could write a funktion to 
compute the normalization factor as described in Schadt et al. and hand it to 
the normalize.AffyBatch.constant() function.  I'm not quite sure if the 
normalize.AffyBatch.qspline() function is the same as the method described in 
the Schadt paper but it looks similar.

Hope that helps,

Quoting Stephen Nyangoma <S.Nyangoma at cs.rug.nl>:

> Hi all,
> I am reading through a paper by 
> Shadt, Li, Su & Wong: Analyzing High- Density Oligonucleotide Gene
> Expression Array Data. Journal of Cellular Biochemistry 80:192-202.
> They discuss linear and spline normalizations. Have these methods been
> implemented in Bioconductor? or has anyone codes implementing
> especially
> the splines method?
> Regards. Stephen.
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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