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

Bioconductor version: 2.9

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>

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


biocViews Microarray, TwoChannel, QualityControl, Preprocessing
Depends R (>= 1.4.1), marray, Biobase
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 dyebiasexamples
Version 1.12.0
Since Bioconductor 2.4 (R-2.9)

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Package Source dyebias_1.12.0.tar.gz
Windows Binary dyebias_1.12.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary dyebias_1.12.0.tgz
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