dyebias: The GASSCO method for correcting for slide-dependent gene-specific dye bias
Version 1.36.0

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)

AuthorPhilip Lijnzaad and Thanasis Margaritis
Bioconductor views Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerPhilip Lijnzaad <plijnzaad@gmail.com>
LicenseGPL-3
Version1.36.0
URL http://www.holstegelab.nl/publications/margaritis_lijnzaad
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("dyebias")

Getting started

Package overview

Popular 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.rgplot: Produce scatterplots of the hybridization, with strongest dye...
See all...

All man pages Function index File listing

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,...

Functions

average.replicates Source code
check.reporter.labels Source code
check.required.columns Source code
check.slide.labels Source code
dyebias Man page
dyebias-package Man page
dyebias.application.subset Man page Source code
dyebias.apply.correction Man page Source code
dyebias.boxplot Man page Source code
dyebias.estimate.iGSDBs Man page Source code
dyebias.maplot Man page Source code
dyebias.monotonicity Man page Source code
dyebias.monotonicityplot Man page Source code
dyebias.rgplot Man page Source code
dyebias.trendplot Man page Source code
find.estimators Source code
limma.to.dataframe Source code
mann.kendall Source code
merge.dyebias Source code
monotonicity Source code
rg.subsets Source code
set.design Source code
set.output Source code
slide.bias Source code
slide.bias.order Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/dyebias.R
R/plotfunctions.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/dyebias-vignette.R
inst/doc/dyebias-vignette.Rnw
inst/doc/dyebias-vignette.pdf
man
man/dyebias-package.Rd
man/dyebias.application.subset.Rd
man/dyebias.apply.correction.Rd
man/dyebias.boxplot.Rd
man/dyebias.estimate.iGSDBs.Rd
man/dyebias.monotonicity.Rd
man/dyebias.monotonicityplot.Rd
man/dyebias.rgplot.Rd
man/dyebias.trendplot.Rd
vignettes
vignettes/ChangeLog
vignettes/dyebias-vignette.Rnw
vignettes/dyebias.bib
vignettes/dyebiasCompleteVignette.pdf
vignettes/gassco.pdf
dyebias documentation built on May 20, 2017, 10:34 p.m.