dyebias

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

Bioconductor version: Release (2.7)

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

To install this package, start R and enter:

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

Documentation

PDF	R Script	dye bias correction
PDF		dyebiasCompleteVignette.pdf
PDF		gassco.pdf

Reference Manual

Details

biocViews	Microarray, TwoChannel, QualityControl, Preprocessing
Depends	R, marray, Biobase
Imports
Suggests	limma, convert, GEOquery, dyebiasexamples, methods
System Requirements
License	GPL-3
URL	http://www.holstegelab.nl/publications/margaritis_lijnzaad
Depends On Me
Imports Me
Suggests Me
Version	1.8.0

Package Downloads

Package Source	dyebias_1.8.0.tar.gz
Windows Binary	dyebias_1.8.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	dyebias_1.8.0.tgz
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