\name{boxplot}
\alias{boxplot}
\alias{boxplot,FeatureSet-method}
\alias{boxplot,ExpressionSet-method}
\title{Boxplot}
\description{
  Boxplot for observed (log-)intensities in a FeatureSet-like object
  (ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet, TilingFeatureSet).
}
\usage{
boxplot(x, \dots)
\S4method{boxplot}{FeatureSet}(x, which=c("pm", "mm", "both"), transfo=log2,
range=0, \dots)
\S4method{boxplot}{ExpressionSet}(x, which, transfo=identity,
range=0, \dots)
}
%- maybe also 'usage' for other objects documented here.

\arguments{
  \item{x}{a \code{FeatureSet}-like object or \code{ExpressionSet}
    object.}
  \item{which}{character defining what probe types are to be used in the
  plot.}
  \item{transfo}{a function to transform the data before plotting. See
    'Details'.}
  \item{range}{this determines how far the plot whiskers extend out from
    the box.  If 'range' is positive, the whiskers extend to the most
    extreme data point which is no more than 'range' times the
    interquartile range from the box. A value of zero causes the
    whiskers to extend to the data extremes.}
  \item{\dots}{arguments to be passed to plot}
}

\details{
  The 'transfo' argument will set the transformation to be used. For raw
  data, 'transfo=log2' is a common practice. For summarized data (which
  are often in log2-scale), no transformation is needed (therefore 'transfo=identity').
  }
\seealso{\code{\link{hist}}, \code{\link{image}}}
%% Add examples
\keyword{hplot}