\name{distributionDistance}
\alias{distributionDistance}
\title{Computes the distribution distance}
\usage{
  distributionDistance(intensityData, method = c("JSDiv",
  "KLDiv", "KLInf"), useSubset = T, subsetFraction = 0.25,
  useQuantileReference = FALSE)
}
\arguments{
  \item{intensityData}{A matrix or an AffyBatch object.}

  \item{method}{The method you want to use.}

  \item{useSubset}{Logical. States if only a subset should
  be used.}

  \item{subsetFraction}{The fraction of the subset.}

  \item{useQuantileReference}{Logical for a quantile
  reference.}
}
\value{
  Computes the distribution distance
}
\description{
  Be aware that this function is implemented quite slow.
}
\examples{
load(system.file("exampleData/normData.RData", package="cn.farms"))
x <- assayData(normData)$intensity[, 1:3]
y <- distributionDistance(x)
attr(y, "Labels") <- substr(sampleNames(normData), 1, 7)
plotDendrogram(y)
}
\author{
  Djork-Arne Clevert \email{okko@clevert.de} and Andreas
  Mitterecker \email{mitterecker@bioinf.jku.at}
}