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dyebias

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

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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 1.63.0
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
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Package Archives

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

Source Package dyebias_1.63.0.tar.gz
Windows Binary dyebias_1.63.0.zip (64-bit only)
macOS Binary (x86_64) dyebias_1.63.0.tgz
macOS Binary (arm64) dyebias_1.63.0.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/
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