\HeaderA{delta.plot}{Delta Plots}{delta.plot}
\keyword{hplot}{delta.plot}
\begin{Description}\relax
Generates both a plot of \eqn{\Delta}{Delta} vs. the FDR and a plot of 
\eqn{\Delta}{Delta} vs. the number of identified genes in a SAM analysis.
\end{Description}
\begin{Usage}
\begin{verbatim}
  delta.plot(object, delta = NULL, helplines = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] a object of class SAM
\item[\code{delta}] a vector of values for \eqn{\Delta}{Delta}. If \code{NULL},
a default set of \eqn{\Delta}{Delta} values will be used 
\item[\code{helplines}] if \code{TRUE}, help lines will be drawn in the
\eqn{\Delta}{Delta} plots
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \eqn{\Delta}{Delta} plots are a visualization of the table generated
by \code{sam} that contains the estimated FDR and the number of identified
genes for a set of \eqn{\Delta}{Delta} values.
\end{Details}
\begin{Value}
Two plots in one graphsheet: The plot of \eqn{\Delta}{Delta} vs. FDR and
the plot of \eqn{\Delta}{Delta} vs. the number of identified genes
\end{Value}
\begin{Note}\relax
SAM was developed by Tusher et al. (2001).

!!! There is a patent pending for the SAM technology at Stanford University. !!!
\end{Note}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{References}\relax
Tusher, V., Tibshirani, R., and Chu, G. (2001). Significance Analysis of
Microarrays Applied to the Ionizing Radiation Response. \emph{PNAS}, 98,
5116-5121.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{SAM-class}{SAM.Rdash.class}},\code{\LinkA{sam}{sam}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}## Not run: 
  # Load the package multtest and the data of Golub et al. (1999)
  # contained in multtest.
  library(multtest)
  data(golub)

  # Perform a SAM analysis.
  sam.out<-sam(golub,golub.cl,B=100,rand=123)
  
  # Generate the Delta plots for the default set of Deltas computed by sam.
  delta.plot(sam.out)
  
  # Another way of generating the same plot.
  plot(sam.out)

  # Generate the Delta plots for Delta = 0.2, 0.4, ..., 2.
  plot(sam.out,seq(0.2,2,0.2))
## End(Not run)\end{ExampleCode}
\end{Examples}