Registration and Call for Abstracts Open for Bioc2024

dyebias

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


Bioconductor version: Release (3.18)

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>

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

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")
dye bias correction PDF R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.62.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License GPL-3
Depends R (>= 1.4.1), marray, Biobase
Imports
System Requirements
URL http://www.holstegelab.nl/publications/margaritis_lijnzaad
See More
Suggests limma, convert, GEOquery, dyebiasexamples, methods
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me dyebiasexamples
Links To Me
Build Report Build Report

Package Archives

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

Source Package dyebias_1.62.0.tar.gz
Windows Binary dyebias_1.62.0.zip
macOS Binary (x86_64) dyebias_1.62.0.tgz
macOS Binary (arm64) dyebias_1.62.0.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