dyebias

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see dyebias.

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

Bioconductor version: 3.1

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 umcutrecht.nl>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dyebias")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("dyebias")

Details

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