\name{plotIntens}
\docType{methods}
\alias{plotIntens}
\alias{plotIntens,ILM-method}
\alias{plotIntens,ILM,character-method}
\title{
plotIntens
}
\description{
Plot the PM intensity and the calculated background of one probe set.
}

\usage{
plotIntens(object,y,z,...)
}
\arguments{
  \item{object}{An object of type \code{\linkS4class{ILM}}}
  \item{y}{A probe set}
  \item{z}{The name of a sample}
  \item{...}{Graphical parameters can be given as arguments to \code{\link[graphics]{par}}}
}

\details{\code{plotIntens} plots one graph for each CEL-file. Note that it is only possible to plot one probe set at a time (if y (or z) is a vector, only the first value is used). If y is missing, no plot is output. If z is missing, the probeset y of first CEL-file is used by default.}

\author{Myriam Kroll and Fabrice Berger}

\seealso{
\code{\linkS4class{ILM}}}

\examples{
file1 <- system.file("rawData","FusionSDK_HG-Focus","HG-Focus","2.Calvin","HG-Focus-1-121502.CEL",package="AffymetrixDataTestFiles")
file2 <- system.file("rawData","FusionSDK_HG-Focus","HG-Focus","2.Calvin","HG-Focus-2-121502.CEL",package="AffymetrixDataTestFiles")
result2 <- ilm(c(file1,file2))
## plot output
plotIntens(result2,"203561_at","HG-Focus-1-121502.CEL")
}

\keyword{ methods }