bioconductor-vsn

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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.

Home http://bioconductor.org/packages/3.6/bioc/html/vsn.html
Versions 3.38.0, 3.44.0, 3.46.0
License Artistic-2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-vsn

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-vsn

and update with:

conda update bioconductor-vsn

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-vsn.