\Header{plotMA}{MA-Plot}
\keyword{hplot}{plotMA}
\begin{Description}\relax
Creates an MA-plot with color coding for various sort of control spots.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotMA(MA,array=1,pch=16,status=NULL,
       values=c("gene","blank","buffer","utility","negative","calibration","ratio"),
       col=c("black","yellow","orange","pink","brown","blue","red"),
       cex=c(0.1,0.6,0.6,0.6,0.6,0.6,0.6))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{MA}] list with components \code{M} containing log-ratios and \code{A} containing average intensities
\item[\code{array}] integer giving the array to be plotted. Corresponds to columns of \code{M} and \code{A}.
\item[\code{pch}] vector or list of plotting characters
\item[\code{status}] character vector giving the control status of each spot on the array.
If \code{NULL} then subsequent arguments are ignored.
\item[\code{values}] character vector giving unique values of \code{status} corresponding to control states of interest
\item[\code{col}] vector of colors, of the same length as \code{values}
\item[\code{cex}] numeric vector of the same length as \code{values} giving sizes for plot symbols
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
See \code{\Link{points}} for possible values for \code{pch}, \code{col} and \code{cex}.
\end{Details}
\begin{Value}
A plot is created on the current graphics device.\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of diagnostic functions available in LIMMA is given in \link{6.Diagnostics}.
\end{SeeAlso}

