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CONSTANd

This is the development version of CONSTANd; for the stable release version, see CONSTANd.

Data normalization by matrix raking


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("CONSTANd")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
CONSTANd HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Cheminformatics, DifferentialExpression, Genetics, MassSpectrometry, Normalization, Preprocessing, Proteomics, Software, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License file LICENSE
Depends R (>= 4.1)
Imports
System Requirements
URL qcquan.net/constand
Bug Reports https://github.com/PDiracDelta/CONSTANd/issues
See More
Suggests BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package CONSTANd_1.11.0.tar.gz
Windows Binary CONSTANd_1.11.0.zip
macOS Binary (x86_64) CONSTANd_1.11.0.tgz
macOS Binary (arm64) CONSTANd_1.11.0.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