\Header{MAList-class}{M-value, A-value Expression List - class}
\keyword{classes}{MAList-class}
\keyword{data}{MAList-class}
\begin{Description}\relax
A simple list-based class for storing M-values and A-values for a batch of spotted microarrays.
\code{MAList} objects are usually created during normalization by the functions \code{\Link{normalizeWithinArrays}} or \code{\Link{MA.RG}}.
\end{Description}
\begin{Section}{Slots/List Components}
\code{MAList} objects can be created by \code{new("MAList",MA)} where \code{MA} is a list.
This class contains no slots (other than \code{.Data}), but objects should contain the following list components:
\Tabular{ll}{
\code{M}:& numeric matrix containing the M-values or log-2 expression ratios.  Rows correspond to spots and columns to arrays.\\
\code{A}:& numeric matrix containing the A-values or average log-2 expression values
}
\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{MAList} objects can be \link[limma:subsetting]{subsetted} and \link[limma:cbind]{combined}.
\code{RGList} objects will return dimensions and hence functions such as \code{\Link{dim}}, \code{\Link{nrow}} and \code{\Link{ncol}} are defined. 
\code{MALists} 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{MAList} objects include
\code{\Link{normalizeWithinArrays}},
\code{\Link{normalizeBetweenArrays}},
\code{\Link{normalizeForPrintorder}},
\code{\Link{plotMA}}
and \code{\Link{plotPrintTipLoess}}.\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{marrayNorm-class}} is the corresponding class in the marrayClasses package.\end{SeeAlso}

