[BioC] Linear and spline normalization

[Laurent Gautier]

There is a bibliographic reference for the qspline reference (which
should be visible when doing "help("normalize.qspline")"... or so it should ;) ).
I am not familiar w/ Shadt et al., so I cannot tell about similarities between
the two...


L.




On Tue, Sep 30, 2003 at 10:46:36AM +0200, Johannes Freudenberg wrote:
> Hi,
> 
> 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,
> Johannes
> 
> 
> 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.
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >
> 
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