\HeaderA{MAplot}{Relative M vs. A plots}{MAplot}
\aliasA{ma.plot}{MAplot}{ma.plot}
\aliasA{MAplot,AffyBatch-method}{MAplot}{MAplot,AffyBatch.Rdash.method}
\aliasA{Mbox}{MAplot}{Mbox}
\aliasA{Mbox,AffyBatch-method}{MAplot}{Mbox,AffyBatch.Rdash.method}
\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,plot.method=c("normal","smoothScatter","add"),add.loess = TRUE,lwd = 1, lty = 1, loess.col = "red",...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An \code{\LinkA{AffyBatch-class}{AffyBatch.Rdash.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{\LinkA{loess}{loess}}.
\item[\code{cex}] Size of text when writing summary statistics on plot
\item[\code{plot.method}] a string specifying how the plot is to be
drawn. \code{"normal"} plots points, \code{"smoothScatter"} uses the
\code{\LinkA{smoothScatter}{smoothScatter}} function. Specifying
\code{"add"} means that the MAplot should be added to the current
plot
\item[\code{add.loess}] add a loess line to the plot
\item[\code{lwd}] width of loess line
\item[\code{lty}] line type for loess line
\item[\code{loess.col}] color for loess line
\end{ldescription}
\end{Arguments}
\begin{SeeAlso}\relax
\code{\LinkA{mva.pairs}{mva.pairs}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if (require(affydata)) {
   data(Dilution)
   MAplot(Dilution)
   Mbox(Dilution)
}
\end{ExampleCode}
\end{Examples}

