\HeaderA{qvalue.cal}{Computation of the q-value}{qvalue.cal}
\keyword{htest}{qvalue.cal}
\begin{Description}\relax
Computes the q-values of a given set of p-values.
\end{Description}
\begin{Usage}
\begin{verbatim}
  qvalue.cal(p, p0, version = 1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{p}] a numeric vector containing the p-values
\item[\code{p0}] a numeric value specifying the prior probability
that a gene is not differentially expressed
\item[\code{version}] If \code{version=2}, the original version of
the q-value, i.e. min\{pFDR\}, will be computed. if
\code{version=1}, min\{FDR\} will be used in the computation
of the q-value
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Using \code{version=1} in \code{qvalue.cal} corresponds to setting
\code{robust=FALSE} in the function \code{qvalue} of John Storey's
\R{} package \pkg{qvalue}, while \code{version=2} corresponds to
\code{robust=TRUE}.
\end{Details}
\begin{Value}
a vector of the same length as \code{p} containing the q-values
corresponding to the p-values in \code{p}
\end{Value}
\begin{Author}\relax
Holger Schwender, \email{holger.schw@gmx.de}
\end{Author}
\begin{References}\relax
Storey, J.D. (2003). The positive False Discovery Rate: A Bayesian
Interpretation and the q-value. \emph{Annals of Statistics}, 31,
2013-2035.

Storey, J.D., and Tibshirani, R. (2003). Statistical Significance for 
Genome-wide Studies. \emph{PNAS}, 100, 9440-9445.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{pi0.est}{pi0.est}},\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)

  # Estimate the prior probability that a gene is not significant.
  pi0<-pi0.est(sam.out@p.value)$p0
  
  # Compute the q-values of the genes.
  q.value<-qvalue.cal(sam.out@p.value,pi0)
## End(Not run)\end{ExampleCode}
\end{Examples}