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.
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.AffyBatch.pspline(). Also a
panel.pspline() is available for adding the smoothed curve to
lattice graphics panels.
The package pspline (S original by Jim Ramsey, R port by Brian Ripley) implements the B-spline/Natural Cubic Spline smoother
Chantal van Leeuwen and Maarten van Iterson Maintainer: Maarten van Iterson<[email protected]>
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.
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