Access the Bioconductor Project Package Repository

A convenient tool to install and update Bioconductor packages.

c(
    person("Martin", "Morgan", email = "martin.morgan@roswellpark.org",
        role = "aut", comment = c(ORCID = "0000-0002-5874-8148")),
    person("Marcel", "Ramos", email = "marcel.ramos@roswellpark.org",
        role = c("ctb", "cre"), comment = c(ORCID = "0000-0002-3242-0582")))

BiocStyle, BiocVersion, remotes, testthat, knitr, withr

Variance stabilization and calibration for microarray data

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

affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat

The package implements a method for normalising microarray intensities, and works
        for 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.

[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.