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
Package: dyebiasexamples
Version: 1.12.0
Date: 2 March 2016
Title: Example data for the dyebias package, which implements the
GASSCO method.
Author: Philip Lijnzaad and Thanasis Margaritis
Description: Data for the dyebias package, consisting of 4 self-self
hybrizations of self-spotted yeast slides, as well as data
from Array Express accession E-MTAB-32
Maintainer: Philip Lijnzaad <plijnzaad@gmail.com>
License: GPL-3
Depends: R (>= 1.4.1), marray, GEOquery
Suggests: dyebias, convert, Biobase
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
biocViews: ExperimentData, SAGEData, CGHData, MicroarrayData,
TwoChannelData, ArrayExpress
NeedsCompilation: no
Packaged: 2016-05-07 20:16:40 UTC; biocbuild
biocViews: Microarray, DifferentialExpression
Package: RBM
Version: 1.4.0
Date: 2014-10-02
Title: RBM: a R package for microarray and RNA-Seq data analysis
Author: Dongmei Li and Chin-Yuan Liang
Maintainer: Dongmei Li <Dongmei_Li@urmc.rochester.edu>
Depends: R (>= 3.2.0), limma, marray
Description: Use A Resampling-Based Empirical Bayes Approach to Assess
Differential Expression in Two-Color Microarrays and RNA-Seq
data sets.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-05-04 06:11:54 UTC; biocbuild
Package: TurboNorm
Type: Package
Title: A fast scatterplot smoother suitable for microarray
normalization
Version: 1.20.0
Date: 2014-18-08
Author: Maarten van Iterson and Chantal van Leeuwen
Maintainer: Maarten van Iterson <mviterson@gmail.com>
Description: A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.
License: LGPL
LazyLoad: yes
Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray
Imports: stats, grDevices, affy, lattice
Suggests: BiocStyle, affydata
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing,
DNAMethylation, CpGIsland, MethylationArray, Normalization
URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html
NeedsCompilation: yes
Packaged: 2016-05-04 03:53:07 UTC; biocbuild
Package: nnNorm
Version: 2.36.0
Date: 2010-04-13
Title: Spatial and intensity based normalization of cDNA microarray
data based on robust neural nets
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Depends: R (>= 2.2.0), marray
Imports: graphics, grDevices, marray, methods, nnet, stats
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Description: This package allows to detect and correct for spatial and intensity biases with two-channel microarray data.
The normalization method implemented in this package is based on robust neural networks fitting.
biocViews: Microarray, TwoChannel, Preprocessing
License: LGPL
URL: http://bioinformaticsprb.med.wayne.edu/tarca/
NeedsCompilation: no
Packaged: 2016-05-04 02:42:48 UTC; biocbuild
providing 
.