Question: Linear and spline normalization
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gravatar for Stephen Nyangoma
16.2 years ago by
Stephen Nyangoma230 wrote:
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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ADD COMMENTlink modified 16.2 years ago by mai98ftu@studserv.uni-leipzig.de140 • written 16.2 years ago by Stephen Nyangoma230
Answer: Linear and spline normalization
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gravatar for mai98ftu@studserv.uni-leipzig.de
16.2 years ago by
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 >
ADD COMMENTlink written 16.2 years ago by mai98ftu@studserv.uni-leipzig.de140
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