\HeaderA{mboxplot-methods}{Box Plots of Relative M Values}{mboxplot.Rdash.methods}
\aliasA{mboxplot}{mboxplot-methods}{mboxplot}
\keyword{methods}{mboxplot-methods}
\begin{Description}\relax
Produce boxplots of relative M values for the set of arrays.

\emph{Usage}

\code{
mboxplot(x, which = "", size = 0, transfo = log2, method  = "mean", range = 0, ylim = c(-1,1), outline = FALSE, names = "namepart", ...)
}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] object of class \code{\LinkA{DataTreeSet}{DataTreeSet}} or \code{\LinkA{ExprTreeSet}{ExprTreeSet}}.
\item[\code{which}] type of probes to be used, for details see \code{\LinkA{validData}{validData}}.
\item[\code{size}] length of sequence to be generated as subset.
\item[\code{transfo}] a valid function to transform the data, usually \dQuote{log2}, or \dQuote{0}.
\item[\code{method}] method to create the reference data, \dQuote{mean} or \dQuote{median}.
\item[\code{range}] determines how far the plot whiskers extend out from the box.
\item[\code{ylim}] range for the plotted y values.
\item[\code{outline}] if \code{outline} is not true, the outliers are not drawn.
\item[\code{names}] optional vector of sample names.
\item[\code{...}] optional arguments to be passed to \code{boxplot}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Create boxplots of M plots, where M is determined relative to a pseudo-mean reference chip.

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 boxplot.
\end{Details}
\begin{Note}\relax
For a \code{\LinkA{DataTreeSet}{DataTreeSet}} object, data must first be attached using method 
\code{\LinkA{attachInten}{attachInten}}.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{boxplot.dev}{boxplot.dev}}, \code{\LinkA{boxplot}{boxplot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

# need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
mboxplot(data.test3, ylim=c(-6,6))
}

# optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)
\end{ExampleCode}
\end{Examples}

