dyebias

Package: dyebias
Title: The GASSCO method for correcting for slide-dependent
gene-specific dye bias
Version: 1.32.0
Date: 2 March 2016
Author: Philip Lijnzaad and Thanasis Margaritis
Description: 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)
Maintainer: Philip Lijnzaad <plijnzaad@gmail.com>
License: GPL-3
Depends: R (>= 1.4.1), marray, Biobase
Suggests: limma, convert, GEOquery, dyebiasexamples, methods
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing
NeedsCompilation: no
Packaged: 2016-05-05 02:02:45 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'dyebias' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'dyebias'
    finding HTML links ... done
    dyebias-package                         html  
    dyebias.application.subset              html  
    dyebias.apply.correction                html  
    dyebias.boxplot                         html  
    dyebias.estimate.iGSDBs                 html  
    dyebias.monotonicity                    html  
    dyebias.monotonicityplot                html  
    dyebias.rgplot                          html  
    dyebias.trendplot                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (dyebias)
Making 'packages.html' ... done