Package: vsn Version: 1.12.0 Date: 16 September 2006 Title: Variance stabilization and calibration for microarray data Author: Wolfgang Huber , contributions from A. von Heydebreck , Markus Ruschhaupt , D. Kostka Maintainer: Wolfgang Huber Depends: R (>= 2.0.0), Biobase (>= 1.4.14) Suggests: affy, affydata, marray, multtest, limma, hgu95av2cdf Description: The package implements a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (aka normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. Reference: [1] Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Wolfgang Huber, Anja von Heydebreck, Holger Süultmann, Annemarie Poustka, Martin Vingron; Bioinformatics (2002) 18 Suppl1 S96-S104. [2] Parameter estimation for the calibration and variance stabilization of microarray data, Wolfgang Huber, Anja von Heydebreck, Holger Sültmann, Annemarie Poustka, and Martin Vingron; Statistical Applications in Genetics and Molecular Biology (2003) Vol. 2 No. 1, Article 3; http://www.bepress.com/sagmb/vol2/iss1/art3. License: Artistic License 2.0 URL: http://www.r-project.org, http://www.ebi.ac.uk/huber biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Packaged: Tue Oct 3 13:57:31 2006; biocbuild Built: R 2.4.0; i486-pc-linux-gnu; 2007-10-23 17:15:54; unix