\name{makeBoxplotControls}
\alias{makeBoxplotControls}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Generate a boxplot of the data vs. the controls }
\description{
  Generates a boxplot of intensity values of negative controls, positive controls and experimental data.
}
\usage{
makeBoxplotControls(header, dataset, channel, plotTitle, showPlot)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{header}{ the header of a dataset file generated with \code{\link{generateDatasetFile}} }
  \item{dataset}{ an R data frame generated with \code{\link{generateDatasetFile}} }
  \item{channel}{ a character string specifying the column whose values will be used for the boxplot }
  \item{plotTitle}{ the plot title }
  \item{showPlot}{ 0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows. }
}

\value{
A boxplot of intensity values of negative controls, positive controls and experimental data will be saved as a pdf and a png file named after the experiment name specified in the header concatenated with the \code{ plotTitle}.

The function returns the plot name.
}

\seealso{ \code{\link{makeBoxplotControlsPerScreen}}, \code{\link{makeBoxplotControlsPerPlate}}, \code{\link{makeBoxplotPerPlate}}, \code{\link{makeBoxplotPerScreen}} }

\examples{
data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

makeBoxplotControls(header, dataset, "SigIntensity", "Data vs. Controls", 1)
}

\keyword{ device }