recipe bioconductor-vsn

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.

Homepage:https://bioconductor.org/packages/3.8/bioc/html/vsn.html License:Artistic-2.0 Recipe:/bioconductor-vsn/meta.yaml Links:biotools: vsn

package bioconductor-vsn

Versions:

3.50.0-0, 3.48.1-0, 3.46.0-0, 3.44.0-0, 3.38.0-1

Depends:

• bioconductor-affy >=1.60.0,<1.61.0
• bioconductor-biobase >=2.42.0,<2.43.0
• bioconductor-limma >=3.38.0,<3.39.0
• libgcc-ng >=7.3.0
• r-base >=3.5.1,<3.5.2.0a0
• r-ggplot2
• r-lattice

Required By:

• bioconductor-mmpalatemirna
• bioconductor-cellhts2
• bioconductor-affypara
• bioconductor-dapar
• bioconductor-ringo
• bioconductor-powerexplorer
• bioconductor-dep
• bcbio-rnaseq
• bioconductor-doscheda
• bioconductor-lvsmirna
• bioconductor-imagehts
• bioconductor-msnbase
• bioconductor-normalyzerde
• r-nanostringnorm
• bioconductor-webbioc
• bioconductor-coexnet
• bioconductor-metaseqr
• r-bcbiornaseq
• bioconductor-pvca
• bioconductor-arrayqualitymetrics
• bioconductor-tilingarray

Installation

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

conda install bioconductor-vsn

and update with:

conda update bioconductor-vsn

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-vsn:<tag>

(see bioconductor-vsn/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-vsn/README.html)