dyebias

DOI: 10.18129/B9.bioc.dyebias    

This package is for version 3.7 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: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dyebias")

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	1.40.0
In Bioconductor since	BioC 2.4 (R-2.9) (9.5 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_1.40.0.tar.gz
Windows Binary	dyebias_1.40.0.zip
Mac OS X 10.11 (El Capitan)	dyebias_1.40.0.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