dyebias

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

Bioconductor version: Development (3.0)

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 <p.lijnzaad at umcutrecht.nl>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("dyebias")

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

Documentation

PDF R Script dye bias correction
PDF   Reference Manual
Text   LICENSE

Details

biocViews Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.23.0
In Bioconductor since BioC 2.4 (R-2.9)
License GPL-3
Depends R (>= 1.4.1), marray, Biobase
Imports
Suggests limma, convert, GEOquery, dyebiasexamples, methods
System Requirements
URL http://www.holstegelab.nl/publications/margaritis_lijnzaad
Depends On Me
Imports Me
Suggests Me dyebiasexamples

Package Downloads

Package Source dyebias_1.23.0.tar.gz
Windows Binary dyebias_1.23.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) dyebias_1.23.0.tgz
Mac OS X 10.9 (Mavericks) dyebias_1.23.0.tgz
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