\name{RGChannelSet-class}
\Rdversion{1.1}
\docType{class}
\alias{RGChannelSet-class}
\alias{RGChannelSetExtended-class}
\alias{show,RGChannelSet-method}
\alias{initialize,RGChannelSet-method}
\alias{initialize,RGChannelSetExtended-method}
\alias{getGreen}
\alias{getRed}
\alias{getManifest}
\title{Class \code{"RGChannelSet"}}
\description{
  These classes represents raw (unprocessed) data from a two color
  micro array; specifically an Illumina methylation array.
}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("RGChannelSet",
  Red, Green, ...)} or
  \code{new("RGChannelSetExtended", Red, Green, RedSD, GreenSD, NBeads, ...)}.
}
\section{Slots}{
  \describe{
    \item{\code{assayData}:}{Object of class \code{"AssayData"}.  A
      \code{RGChannelSet} contains elements with names \code{Green} and
      \code{Red} and a \code{"RGChannelSetExtended"} additionally adds
      \code{GreenSD}, \code{RedSD} and \code{NBeads}.}
    \item{\code{phenoData}:}{Object of class \code{"AnnotatedDataFrame"}.}
    \item{\code{featureData}:}{Object of class \code{"AnnotatedDataFrame"}.}
    \item{\code{experimentData}:}{Object of class \code{"MIAxE"}.}
    \item{\code{annotation}:}{Object of class \code{"character"}.
      Contains the array name (without \code{"manifest"}.)}
    \item{\code{protocolData}:}{Object of class \code{"AnnotatedDataFrame"}.}
    \item{\code{.__classVersion__}:}{Object of class \code{"Versions"}.}
  }
}
\section{Extends}{
Class \code{"\linkS4class{eSet}"}, directly.
Class \code{"\linkS4class{VersionedBiobase}"}, by class \code{"eSet"}, distance 2.
Class \code{"\linkS4class{Versioned}"}, by class \code{"eSet"}, distance 3.
}
\section{Utilities}{
  \describe{
    \item{\code{show}:}{The show method.}
    \item{\code{initialize}:}{The initialize method, see above.}
    \item{\code{getGreen}:}{Gets the Green channel as a matrix.}
    \item{\code{getRed}:}{Gets the Red channel as a matrix.}
    \item{\code{getManifest}:}{Gets the manifest object associated with
      the array type}
  }
}
\author{
  Kasper Daniel Hansen \email{khansen@jhsph.edu}.
}
\seealso{
  See \code{\linkS4class{eSet}} for the basic class that is used as a
  building block for \code{"RGChannelSet(Extended)"}.  See
  \code{\linkS4class{IlluminaMethylationManifest}} for a class
  representing the design of the array.
}
\examples{
showClass("RGChannelSet")
}
\keyword{classes}