TurboNorm (version 1.20.0)

TurboNorm-package: 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.

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