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dyebias

 

   

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

Bioconductor version: Release (3.3)

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 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

Details

biocViews Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.32.0
In Bioconductor since BioC 2.4 (R-2.9) (7.5 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
Build Report  

Package Archives

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Package Source dyebias_1.32.0.tar.gz
Windows Binary dyebias_1.32.0.zip
Mac OS X 10.9 (Mavericks) dyebias_1.32.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/dyebias/tree/release-3.3
Package Short Url http://bioconductor.org/packages/dyebias/
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