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)

Author
Philip Lijnzaad and Thanasis Margaritis
Date of publication
None
Maintainer
Philip Lijnzaad <plijnzaad@gmail.com>
License
GPL-3
Version
1.34.0
URLs

View on Bioconductor

Man pages

dyebias.application.subset
Return a subset of reporters that can be dye bias-corrected...
dyebias.apply.correction
Perform dye bias correction using the GASSCO method
dyebias.boxplot
Creates boxplots of the reporters with the strongest dye bias
dyebias.estimate.iGSDBs
Estimate intrinsic gene specific dye biases (part of the...
dyebias.monotonicity
Calculate the degree of monotonicity of the dye bias across...
dyebias.monotonicityplot
Show the degree of monotonicity of the dye bias across the...
dyebias-package
The GASSCO method for correcting for slide-dependent...
dyebias.rgplot
Produce scatterplots of the hybridization, with strongest dye...
dyebias.trendplot
Creates a trend-plot of all reporters, binned by dye bias,...

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