vsn/DESCRIPTION at devel · Huber-group-EMBL/vsn · GitHub

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Package: vsn
Version: 3.81.1
Title: Variance stabilization and calibration for microarray data
Authors@R: c(
    person("Wolfgang", "Huber", email="wolfgang.huber@embl.org", role = c("aut","cre")),
    person("Anja", "von Heydebreck", role = c("aut")),
    person("Dennis", "Kostka", role = c("ctb")),
    person("David", "Kreil", role = c("ctb")),
    person("Hans-Ulrich", "Klein", role = c("ctb")),
    person("Robert", "Gentleman", role = c("ctb")),
    person("Deepayan", "Sarkar", role = c("ctb")),
    person("Gordon", "Smyth", role = c("ctb")),
    person("Federal Ministry of Research, Technology and Space of Germany, DHGP", role="fnd"))
Maintainer: Wolfgang Huber <wolfgang.huber@embl.org>
Depends: R (>= 4.0.0), methods, Biobase
Imports: affy, limma, lattice, ggplot2
Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat, hexbin
Description: The package implements a method for normalising microarray intensities from single- and
        multiple-color arrays. It can also be used
	for data from other technologies, as long as they have similar format. The method uses a
	robust variant of the maximum-likelihood estimator for an additive-multiplicative error
	model and affine calibration. The model incorporates data calibration step (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: https://github.com/Huber-group-EMBL/vsn, https://huber-group-embl.github.io/vsn/
BugReports: https://github.com/Huber-group-EMBL/vsn/issues
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
VignetteBuilder: knitr
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
	normalize.AffyBatch.vsn.R sagmbSimulateData.R  zzz.R
RoxygenNote: 7.3.3