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@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@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent