vsn

Package: vsn
Version: 3.40.0
Title: Variance stabilization and calibration for microarray data
Author: Wolfgang Huber, with contributions from Anja von
Heydebreck. Many comments and suggestions by users are
acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich
Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth
Maintainer: Wolfgang Huber <whuber@embl.de>
Depends: R (>= 2.10), Biobase
Imports: methods, affy, limma, lattice, ggplot2 (>= 2.0.0), hexbin
Suggests: affydata, hgu95av2cdf
Description: The package implements a method for normalising microarray intensities,
both between colours within array, and between arrays. The method uses a
robust variant of the maximum-likelihood estimator for the stochastic model of
microarray data described in the references (see vignette).
The model incorporates data calibration (a.k.a. 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
Sueltmann, 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 Sueltmann,
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-2.0
URL: http://www.r-project.org
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Collate: AllClasses.R AllGenerics.R vsn2.R vsnLogLik.R justvsn.R
methods-vsnInput.R methods-vsn.R methods-vsn2.R
methods-predict.R RGList_to_NChannelSet.R meanSdPlot-methods.R
plotLikelihood.R vsnPlotPar.R vsn.R vsnh.R getIntensityMatrix.R
normalize.AffyBatch.vsn.R sagmbSimulateData.R zzz.R
NeedsCompilation: yes
Packaged: 2016-05-04 02:38:02 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'vsn' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vsn.c -o vsn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c vsn2.c -o vsn2.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o vsn.so init.o vsn.o vsn2.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/vsn/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'logLik' from package 'stats' in package 'vsn'
Creating a generic function for 'coef' from package 'stats' in package 'vsn'
Creating a generic function for 'coefficients' from package 'stats' in package 'vsn'
** help
*** installing help indices
  converting help for package 'vsn'
    finding HTML links ... done
    class.vsn                               html  
    class.vsnInput                          html  
    justvsn                                 html  
    kidney                                  html  
    lymphoma                                html  
    meanSdPlot                              html  
Rd warning: /tmp/RtmpsrxMNb/R.INSTALL5a216a3a4f/vsn/man/meanSdPlot.Rd:43: missing file link 'stat_binhex'
Rd warning: /tmp/RtmpsrxMNb/R.INSTALL5a216a3a4f/vsn/man/meanSdPlot.Rd:44: missing file link 'stat_binhex'
    normalize.AffyBatch.vsn                 html  
    sagmbSimulateData                       html  
    scalingFactorTransformation             html  
    vsn-package                             html  
    vsn                                     html  
    vsn2                                    html  
    vsn2trsf                                html  
    vsnLikelihood                           html  
    vsnPlotPar                              html  
    vsnh                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vsn)
Making 'packages.html' ... done