CONSTANd

DOI: 10.18129/B9.bioc.CONSTANd  

Data normalization by matrix raking

Bioconductor version: Release (3.16)

Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.

Author: Joris Van Houtven [aut, trl], Geert Jan Bex [trl], Dirk Valkenborg [aut, cre]

Maintainer: Dirk Valkenborg <dirk.valkenborg at uhasselt.be>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CONSTANd")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CONSTANd")

 

HTML	R Script	CONSTANd
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Cheminformatics, DifferentialExpression, Genetics, MassSpectrometry, Normalization, Preprocessing, Proteomics, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	file LICENSE
Depends	R (>= 4.1)
Imports
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma
SystemRequirements
Enhances
URL	qcquan.net/constand
BugReports	https://github.com/PDiracDelta/CONSTANd/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CONSTANd_1.6.0.tar.gz
Windows Binary	CONSTANd_1.6.0.zip
macOS Binary (x86_64)	CONSTANd_1.6.0.tgz
macOS Binary (arm64)	CONSTANd_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CONSTANd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CONSTANd
Bioc Package Browser	https://code.bioconductor.org/browse/CONSTANd/
Package Short Url	https://bioconductor.org/packages/CONSTANd/
Package Downloads Report	Download Stats