\HeaderA{getEAWP}{Extract Basic Data from Microarray Data Objects}{getEAWP}
\keyword{array}{getEAWP}
\begin{Description}\relax
Given a microarray data object of any known class, get the expression values, weights, probe annotation and A-values, which are needed for linear modelling.
This function is called by the linear modelling functions in LIMMA.
\end{Description}
\begin{Usage}
\begin{verbatim}
getEAWP(object)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] a microarray data object.
An object of class \code{list}, \code{MAList}, \code{EList}, \code{marrayNorm}, \code{PLMset}, \code{vsn}, or any class inheriting from \code{ExpressionSet}, or any object that can be coerced to a numeric matrix.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
In the case of two-color objects, the \code{Amean} is computed from the matrix of A-values.
For single-channel objects, \code{Amean} is computed from the matrix of expression vales.
\code{PLMset}, \code{vsn} and \code{ExpressionSet} are assumed to be single-channel for this purpose.

If \code{object} is a matrix, it is assumed to contain log-intensities if the values are all positive and log-ratios otherwise.
\code{Amean} is computed in the former case but not the latter.
\end{Details}
\begin{Value}
A list with components
\begin{ldescription}
\item[\code{exprs}] numeric matrix of log-ratios or log-intensities
\item[\code{weights}] numeric matrix of weights
\item[\code{probes}] data.frame of probe-annotation
\item[\code{Amean}] numeric vector of average log-expression for each probe
\end{ldescription}
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
\LinkA{02.Classes}{02.Classes} gives an overview of data classes used in LIMMA.
\end{SeeAlso}

