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

Bioconductor version: Release (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>

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PDF R Script dye bias correction
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biocViews Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.24.0
In Bioconductor since BioC 2.4 (R-2.9)
License GPL-3
Depends R (>= 1.4.1), marray, Biobase
Suggests limma, convert, GEOquery, dyebiasexamples, methods
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Depends On Me
Imports Me
Suggests Me dyebiasexamples

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