\HeaderA{mdplot}{mdplot}{mdplot}
\keyword{hplot}{mdplot}
\begin{Description}\relax
Creates a mean-difference plot.
\end{Description}
\begin{Usage}
\begin{verbatim}
mdplot(x, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] numeric \code{matrix} with at least two columns
\item[\code{...}] any other arguments are passed to \code{plot}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Plots differences vs means for a set of bivariate values.
This is useful to contrast expression values for two microarrays.

Note that an MA-plot \code{\LinkA{plotMA}{plotMA}} is a type of mean-difference plot.
\end{Details}
\begin{Value}
A plot is created on the current graphics device.
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{References}\relax
Chambers, J. M., Cleveland, W. S., Kleiner, B., and Tukey, P. A. (1983). Graphical Methods of Data Analysis. Wadsworth (pp. 48-57).

Cleveland, W. S., (1993). Visualizing Data. Hobart Press.

Bland, J. M., and Altman, D. G. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. Lancet i, 307-310.

See also \url{http://www.statsci.org/micrarra/refs/maplots.html}
\end{References}
\begin{SeeAlso}\relax
An overview of diagnostic functions available in LIMMA is given in \LinkA{09.Diagnostics}{09.Diagnostics}.
\end{SeeAlso}