dyebias

DOI: 10.18129/B9.bioc.dyebias  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see dyebias.

The GASSCO method for correcting for slide-dependent gene-specific dye bias

Bioconductor version: 3.17

Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)

Author: Philip Lijnzaad and Thanasis Margaritis

Maintainer: Philip Lijnzaad <plijnzaad at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("dyebias")

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("dyebias")

 

PDF	R Script	dye bias correction
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version	1.60.0
In Bioconductor since	BioC 2.4 (R-2.9) (14.5 years)
License	GPL-3
Depends	R (>= 1.4.1), marray, Biobase
Imports
LinkingTo
Suggests	limma, convert, GEOquery, dyebiasexamples, methods
SystemRequirements
Enhances
URL	http://www.holstegelab.nl/publications/margaritis_lijnzaad
Depends On Me
Imports Me
Suggests Me	dyebiasexamples
Links To Me
Build Report

Package Archives

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

Source Package	dyebias_1.60.0.tar.gz
Windows Binary	dyebias_1.60.0.zip
macOS Binary (x86_64)	dyebias_1.60.0.tgz
macOS Binary (arm64)	dyebias_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dyebias
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dyebias
Bioc Package Browser	https://code.bioconductor.org/browse/dyebias/
Package Short Url	https://bioconductor.org/packages/dyebias/
Package Downloads Report	Download Stats