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

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)

Package details

AuthorPhilip Lijnzaad and Thanasis Margaritis
Bioconductor views Microarray Preprocessing QualityControl TwoChannel
MaintainerPhilip Lijnzaad <plijnzaad@gmail.com>
URL http://www.holstegelab.nl/publications/margaritis_lijnzaad
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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dyebias documentation built on Nov. 8, 2020, 5:53 p.m.