TurboNorm-package {TurboNorm} | R Documentation

## A fast scatterplot smoother with applications for microarray normalization

### Description

A fast scatterplot smoother based on B-splines with second order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.

### Details

Package: | TurboNorm
Type: | Package
Version: | 1.7.2
Date: | 2013-29-01
License: | LGPL
LazyLoad: | yes

This package contains an implementation of piecewise constant P-splines of Eilers and Marx (1996) that can be used for normalization of either single- or two-colour data. For two-colour data objects of type `RGList` from the `limma` package and `MarrayRaw` from the package `marray` can be normalized using the function `pspline()`. For single colour microarray data wrapper functions are written based on the `affy` package functions `normalize.loess()` and `normalize.AffyBatch.loess()` namely `normalize.pspline()` and `normalize.AffyBatch.pspline()`. Also a `panel.pspline()` is available for adding the smoothed curve to `lattice` graphics panels.

### Note

The package pspline (S original by Jim Ramsey, R port by Brian Ripley) implements the B-spline/Natural Cubic Spline smoother

### Author(s)

Chantal van Leeuwen and Maarten van Iterson Maintainer: Maarten van Iterson<mviterson@gmail.com>

### References

van Iterson M, Duijkers FA, Meijerink JP, Admiraal P, van Ommen GJ, Boer JM, van Noesel MM, Menezes RX (2012). A novel and fast normalization method for high-density arrays. SAGMB, 11(4).

Paul .H.C. Eilers and Brain D. Marx (1996). Flexible smoothing with B-splines and Penalties. Statistical Science, Vol 11, No. 2, 89-121.

### See Also

`turbotrend, pspline, normalize.pspline, normalize.AffyBatch.pspline, panel.pspline`

[Package TurboNorm version 1.40.0 Index]