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)

AuthorPhilip Lijnzaad and Thanasis Margaritis
Date of publicationNone
MaintainerPhilip Lijnzaad <plijnzaad@gmail.com>
LicenseGPL-3
Version1.34.0
http://www.holstegelab.nl/publications/margaritis_lijnzaad

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Files in this package

dyebias/DESCRIPTION
dyebias/LICENSE
dyebias/NAMESPACE
dyebias/R
dyebias/R/dyebias.R dyebias/R/plotfunctions.R
dyebias/build
dyebias/build/vignette.rds
dyebias/inst
dyebias/inst/CITATION
dyebias/inst/doc
dyebias/inst/doc/dyebias-vignette.R
dyebias/inst/doc/dyebias-vignette.Rnw
dyebias/inst/doc/dyebias-vignette.pdf
dyebias/man
dyebias/man/dyebias-package.Rd dyebias/man/dyebias.application.subset.Rd dyebias/man/dyebias.apply.correction.Rd dyebias/man/dyebias.boxplot.Rd dyebias/man/dyebias.estimate.iGSDBs.Rd dyebias/man/dyebias.monotonicity.Rd dyebias/man/dyebias.monotonicityplot.Rd dyebias/man/dyebias.rgplot.Rd dyebias/man/dyebias.trendplot.Rd
dyebias/vignettes
dyebias/vignettes/ChangeLog
dyebias/vignettes/dyebias-vignette.Rnw
dyebias/vignettes/dyebias.bib
dyebias/vignettes/dyebiasCompleteVignette.pdf
dyebias/vignettes/gassco.pdf

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