turbonorm-package: A fast scatterplot smoother with applications for microarray...

Description Details Note Author(s) References See Also

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<[email protected]>

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


Bioconductor-mirror/TurboNorm documentation built on June 1, 2017, 3:25 a.m.