Package vsn

Detailed Description

Title:Variance stabilization and calibration for microarray data 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.

Author:Wolfgang Huber <huber@ebi.ac.uk>, contributions from A. von Heydebreck <heydebre@molgen.mpg.de>, Markus Ruschhaupt <m.ruschhaupt@dkfz-heidelberg.de>, D. Kostka <dennis.kostka@molgen.mpg.de> Maintainer:Wolfgang Huber <huber@ebi.ac.uk> Version:1.8.0 Built:R 2.2.1; i486-pc-linux-gnu; 2006-03-04 19:53:21; unix Date:18 Sep 2005 Depends:R (>= 2.0.0), Biobase (>= 1.4.14) License:LGPL Packaged:Mon Oct 17 00:04:26 2005; biocbuild Suggests:affy, affydata, marray, multtest, limma, hgu95av2cdf URL:http://www.r-project.org, http://www.ebi.ac.uk/huber

kidney
Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
lastPlot.jpeg

Last ouput from kidney(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: vsn/kidney/example.log
meanSdPlot
Plot row standard deviations versus row means
lastPlot.jpeg

Last ouput from meanSdPlot(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: vsn/meanSdPlot/example.log

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