recipe bioconductor-vsn

Variance stabilization and calibration for microarray data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/vsn.html

License

Artistic-2.0

Recipe

/bioconductor-vsn/meta.yaml

Links

biotools: 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.

package bioconductor-vsn

Versions

3.56.0-0,  3.54.0-0,  3.52.0-1,  3.50.0-0,  3.48.1-0,  3.46.0-0,  3.44.0-0,  3.38.0-1

Depends

• bioconductor-affy >=1.66.0,<1.67.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-limma >=3.44.0,<3.45.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-lattice

Required By

• bioconductor-metaseqr2

• bioconductor-msnbase

• bioconductor-tilingarray

• bioconductor-ringo

• bioconductor-dep

• bioconductor-webbioc

• bioconductor-pvca

• r-nanostringnorm

• bioconductor-doscheda

• bioconductor-affypara

• bioconductor-metaseqr

• bioconductor-coexnet

• bioconductor-cellhts2

• bioconductor-mmpalatemirna

• bcbio-rnaseq

• bioconductor-powerexplorer

• r-bcbiornaseq

• bioconductor-arrayqualitymetrics

• bioconductor-imagehts

• bioconductor-normalyzerde

• bioconductor-dapar

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)