\Header{MAplot}{Relative M vs. A plots}
\alias{ma.plot}{MAplot}
\alias{MAplot,AffyBatch-method}{MAplot}
\alias{Mbox}{MAplot}
\alias{Mbox,AffyBatch-method}{MAplot}
\keyword{hplot}{MAplot}
\begin{Description}\relax
Create boxplots of M or M vs A plots. Where M is determined relative
to a specified chip or to a pseudo-median reference chip.
\end{Description}
\begin{Usage}
\begin{verbatim}
MAplot(object,...)
Mbox(object,...)
ma.plot(A,M,subset=sample(1:length(M),min(c(10000, length(M)))),show.statistics=TRUE,span=2/3,family.loess="gaussian",cex=2,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An \code{\Link{AffyBatch-class}}
\item[\code{...}] Additional parameters for the routine
\item[\code{A}] A vector to plot along the horizonal axis
\item[\code{M}] A vector to plot along vertical axis
\item[\code{subset}] A set of indices to use when drawing the loess curve
\item[\code{show.statistics}] If true some summary statistics of the M values
are drawn
\item[\code{span}] span to be used for loess fit.
\item[\code{family.loess}] \code{"guassian"} or \code{"symmetric"} as in
\code{\Link{loess}}.
\item[\code{cex}] Size of text when writing summary statistics on plot
\end{ldescription}
\end{Arguments}
\begin{SeeAlso}\relax
\code{\Link{mva.pairs}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
   data(affybatch.example)
   MAplot(affybatch.example)
   Mbox(affybatch.example)
\end{ExampleCode}
\end{Examples}

