R/999.package.R

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

#########################################################################/**
# @RdocPackage aroma.light
#
# \encoding{latin1}
#
# \description{
#   @eval "getDescription(aroma.light)"
# }
#
# \section{Installation}{
#   To install this package, see
#   \url{http://bioconductor.org/packages/release/bioc/html/aroma.light.html}.
# }
#
# \section{To get started}{
#   For scanner calibration:
#   \enumerate{
#     \item see @see "calibrateMultiscan" - scan the same array two or more times to calibrate for scanner effects and extended dynamical range.
#   }
#
#   To normalize multiple single-channel arrays all with the same number of probes/spots:
#   \enumerate{
#     \item @see "normalizeAffine" - normalizes, on the intensity scale,  for differences in offset and scale between channels.
#     \item @see "normalizeQuantileRank", @see "normalizeQuantileSpline" - normalizes, on the intensity scale,  for differences in empirical distribution between channels.
#   }
#
#   To normalize multiple single-channel arrays with varying number probes/spots:
#   \enumerate{
#     \item @see "normalizeQuantileRank", @see "normalizeQuantileSpline" - normalizes, on the intensity scale, for differences in empirical distribution between channels.
#   }
#
#   To normalize two-channel arrays:
#   \enumerate{
#     \item @see "normalizeAffine" - normalizes, on the intensity scale, for differences in offset and scale between channels.  This will also correct for intensity-dependent affects on the log scale.
#     \item @see "normalizeCurveFit" - Classical intensity-dependent normalization, on the log scale, e.g. lowess normalization.
#   }
#
#   To normalize three or more channels:
#   \enumerate{
#     \item @see "normalizeAffine" - normalizes, on the intensity scale, for differences in offset and scale between channels.  This will minimize the curvature on the log scale between any two channels.
#   }
# }
#
# \section{Further readings}{
#   Several of the normalization methods proposed in [1]-[7] are
#   available in this package.
# }
#
# \section{How to cite this package}{
#   Whenever using this package, please cite one or more of [1]-[7].
# }
#
# \section{Wishlist}{
#  Here is a list of features that would be useful, but which I have
#  too little time to add myself. Contributions are appreciated.
#  \itemize{
#    \item At the moment, nothing.
#  }
#
#  If you consider to contribute, make sure it is not already
#  implemented by downloading the latest "devel" version!
# }
#
# @author "*"
#
# \section{License}{
#   The releases of this package is licensed under
#   GPL version 2 or newer.
#
#   NB: Except for the \code{robustSmoothSpline()} method,
#   it is alright to distribute the rest of the package under
#   LGPL version 2.1 or newer.
#
#   The development code of the packages is under a private licence
#   (where applicable) and patches sent to the author fall under the
#   latter license, but will be, if incorporated, released under the
#   "release" license above.
# }
#
# \references{
#  Some of the reference below can be found at
#  \url{http://www.aroma-project.org/publications/}.\cr
#
# [1] H. Bengtsson, \emph{Identification and normalization of plate effects
#     in cDNA microarray data}, Preprints in Mathematical Sciences,
#     2002:28, Mathematical Statistics, Centre for Mathematical Sciences,
#     Lund University, 2002.\cr
#
# [2] @include "../incl/BengtssonH_2003.bib.Rdoc" \cr
#
# [3] H. Bengtsson, \emph{aroma - An R Object-oriented Microarray
#     Analysis environment}, Preprints in Mathematical Sciences (manuscript
#     in preparation), Mathematical Statistics, Centre for Mathematical
#     Sciences, Lund University, 2004.\cr
#
# [4] @include "../incl/BengtssonH_etal_2004.bib.Rdoc" \cr
#
# [5] @include "../incl/BengtssonHossjer_2006.bib.Rdoc" \cr
#
# [6] @include "../incl/BengtssonH_etal_2008.bib.Rdoc" \cr
#
# [7] @include "../incl/BengtssonH_etal_2009.bib.Rdoc" \cr
#
# [8] @include "../incl/BengtssonNeuvial_2010.bib.Rdoc" \cr
# }
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