\Header{RGList-class}{Red, Green Intensity List - class}
\keyword{classes}{RGList-class}
\keyword{data}{RGList-class}
\begin{Description}\relax
A simple list-based class for storing red and green channel foreground and background intensities for a batch of spotted microarrays.
\code{RGList} objects are normally created by \code{\Link{read.maimages}}.
\end{Description}
\begin{Section}{Slots/List Components}
\code{RGList} objects can be created by \code{new("RGList",RG)} where \code{RG} is a list.
Objects of this class contains no slots (other than \code{.Data}), but objects should contain the following list components:
\Tabular{ll}{
\code{R}:& numeric matrix containing the red (cy5) foreground intensities.  Rows correspond to spots and columns to arrays.\\
\code{G}:& numeric matrix containing the green (cy3) foreground intensities\\
\code{Rb}:& numeric matrix containing the red (cy5) background intensities\\
\code{Gb}:& numeric matrix containing the green (cy3) background intensities
}
Optional components include
\Tabular{ll}{
\code{weights}:& numeric matric containing relative spot quality weights.  Should be non-negative.\\
\code{printer}:& list containing information on the process used to print the spots on the arrays.  See \link[limma:PrintLayout]{PrintLayout}.\\
\code{genes}:& data.frame containing information on the genes spotted on the arrays.  Should include a character column \code{Name} containing names for the genes or controls.\\
\code{targets}:& data.frame containing information on the target RNA samples.  Should include factor or character columns \code{Cy3} and \code{Cy5} specifying which RNA was hybridized to each array.
}
All of the matrices should have the same dimensions.
The row dimension of \code{targets} should match the column dimension of the matrices.\end{Section}
\begin{Section}{Methods}
This class inherits directly from class \code{list} so any operation appropriate for lists will work on objects of this class.
In addition, \code{RGList} objects can be \link[limma:subsetting]{subsetted}, \link[limma:cbind]{combined} and \link[limma:merge]{merged}.
\code{RGList} objects will return dimensions and hence functions such as \code{\Link{dim}}, \code{\Link{nrow}} and \code{\Link{ncol}} are defined. 
\code{RGLists} also inherit a \code{\Link{show}} method from the virtual class \code{\Link{LargeDataObject}}, which means that \code{RGLists} will print in a compact way.

Other functions in LIMMA which operate on \code{RGList} objects include
\code{\Link{normalizeBetweenArrays}},
\code{\Link{normalizeForPrintorder}},
\code{\Link{normalizeWithinArrays}}.\end{Section}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\link{2.Classes} gives an overview of all the classes defined by this package.

\code{\Link{marrayRaw-class}} is the corresponding class in the marrayClasses package.\end{SeeAlso}

