R/999.package.R

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

#########################################################################/**
# @RdocPackage aroma
#
# \encoding{latin1}
# 
# \description{
#   @eval "getDescription(aroma)" 
#
#   This package was formerly known as the \pkg{com.braju.sma} package.
#   On 2003-12-31 it was renamed to the current name \pkg{aroma}, which
#   is an achronym for \emph{An R Object-oriented Microarray Analysis} 
#   package.
# }
#
# \section{Requirements}{
#   This package depends on several other packages, namely
#   \pkg{R.methodsS3}, \pkg{R.oo}, \pkg{R.utils}, \pkg{aroma.light},
#   \pkg{R.basic}, \pkg{R.graphics}, and \pkg{R.io}.
# } 
#
# \section{Installation}{
#   To install this package and all required package, see instructions at
#   \url{http://www.braju.com/R/}.\cr
# }
#
# \section{To get started}{
#   To get started, see:
#   \enumerate{
#     \item @see "GenePixData", @see "QuantArrayData", @see "ScanAlyzeData", 
#           @see "SpotData", or @see "SpotfinderData".
#     \item For an overview of normalization and calibration methods,
#           please see the @see "aroma.light::aroma.light" package.
#     \item @see "calibrateMultiscan.RGData".
#     \item @see "normalizeAffine.RGData".
#   }
# }
# 
# \section{Further readings}{
#   For an overview of \pkg{aroma}, see [1]. 
#   See also the online webpage of \code{aroma} - 
#   \url{http://www.maths.lth.se/help/R/aroma/}.
#   Several of the normalization methods proposed in [3]-[5] are 
#   available in this package.
# } 
#
# \section{How to cite this package}{
#   Whenever using this package, please cite [1] as\cr
#
#   @howtocite "aroma"
# }
#
# @author
#
# \references{
#  Some of the reference below can be found at 
#  \url{http://www.maths.lth.se/bioinformatics/publications/}.\cr
#
# [1] 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
#
# [2] @include "../incl/BengtssonH_2003.bib.Rdoc" \cr
#
# [3] @include "../incl/BengtssonHossjer_2006.bib.Rdoc" \cr
#
# [4] @include "../incl/BengtssonH_etal_2004.bib.Rdoc" \cr
#
# [5] 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
# }
#*/#########################################################################