DOI: 10.18129/B9.bioc.dyebias    

This package is for version 3.8 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: 3.8

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")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

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


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



PDF R Script dye bias correction
PDF   Reference Manual


biocViews Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.42.0
In Bioconductor since BioC 2.4 (R-2.9) (10 years)
License GPL-3
Depends R (>= 1.4.1), marray, Biobase
Suggests limma, convert, GEOquery, dyebiasexamples, methods
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_1.42.0.tar.gz
Windows Binary dyebias_1.42.0.zip
Mac OS X 10.11 (El Capitan) dyebias_1.42.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dyebias
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dyebias
Package Short Url http://bioconductor.org/packages/dyebias/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: