\HeaderA{mvaplot-methods}{M vs A Plot}{mvaplot.Rdash.methods}
\aliasA{mvaplot}{mvaplot-methods}{mvaplot}
\keyword{methods}{mvaplot-methods}
\begin{Description}\relax
Produce scatter plots of M values vs A values of the samples.

\emph{Usage}

\code{
mvaplot(x, transfo = log2, method  = "median", names = "namepart", ylim = c(-6,6), ...)
}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.
\item[\code{transfo}] a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.
\item[\code{method}] method to compute M, \dQuote{mean} or \dQuote{median}.
\item[\code{names}] optional vector of sample names.
\item[\code{ylim}] range for the plotted M values.
\item[\code{...}] optional arguments to be passed to \code{plot}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Produces mvaplots for slot \code{data} for an object of class \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.

For \code{names=NULL} full column names of slot \code{data} will be displayed while for 
\code{names="namepart"} column names will be displayed without name extension. If \code{names}
is a vector of column names, only these columns will displayed as mvaplot.
\end{Details}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{mvaplot.dev}{mvaplot.dev}}
\end{SeeAlso}

