\HeaderA{as.matrix}{Turn a Microarray Data Object into a Matrix}{as.matrix}
\methaliasA{as.matrix.ExpressionSet}{as.matrix}{as.matrix.ExpressionSet}
\methaliasA{as.matrix.LumiBatch}{as.matrix}{as.matrix.LumiBatch}
\methaliasA{as.matrix.MAList}{as.matrix}{as.matrix.MAList}
\methaliasA{as.matrix.MArrayLM}{as.matrix}{as.matrix.MArrayLM}
\methaliasA{as.matrix.marrayNorm}{as.matrix}{as.matrix.marrayNorm}
\methaliasA{as.matrix.PLMset}{as.matrix}{as.matrix.PLMset}
\methaliasA{as.matrix.RGList}{as.matrix}{as.matrix.RGList}
\methaliasA{as.matrix.vsn}{as.matrix}{as.matrix.vsn}
\keyword{array}{as.matrix}
\begin{Description}\relax
Turn a microarray data object into a numeric matrix by extracting the expression values.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'MAList':
as.matrix(x,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] an object of class \code{RGList}, \code{MAList}, \code{MArrayLM}, \code{marrayNorm}, \code{PLMset}, \code{ExpressionSet}, \code{LumiBatch} or \code{vsn}.
\item[\code{...}] additional arguments, not used for these methods.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These methods extract the matrix of log-ratios, for \code{MAList} or \code{marrayNorm} objects, or the matrix of expression values for other expression objects such as \code{ExressionSet}.
For \code{MArrayLM} objects, the matrix of fitted coefficients is extracted.

These methods involve loss of information, so the original data object is not recoverable.
\end{Details}
\begin{Value}
A numeric matrix.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{as.matrix}{as.matrix}} in the base package or \code{\LinkA{exprs}{exprs}} in the Biobase package.

\LinkA{02.Classes}{02.Classes} gives an overview of data classes used in LIMMA.
\end{SeeAlso}

