\HeaderA{fudge2}{Fudge Factor}{fudge2}
\keyword{optimize}{fudge2}
\begin{Description}\relax
Computes the fudge factor as described by Tusher et al. (2001).
\end{Description}
\begin{Usage}
\begin{verbatim}
  fudge2(r, s, alpha = seq(0, 1, 0.05), include.zero = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{r}] a numeric vector. The numerator of the test statistic computed
for each gene is represented by one component of this vector
\item[\code{s}] a numeric vector. Each component of this vector corresponds
to the denominator of the test statistic of a gene
\item[\code{alpha}] a numeric value or vector specifying quantiles of the
\code{s} values. If \code{alpha} is numeric, this quantile of \code{s}
will be used as fudge factor. Otherwise, the \code{alpha} quantile
of the \code{s} values is computed that is optimal following the criterion
of Tusher et al. (2001)
\item[\code{include.zero}] If \code{TRUE}, \eqn{s_0=0}{s0=0} is also a possible
choice for the fudge factor
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{s.zero}] the value of the fudge factor \eqn{s_0}{s0}
\item[\code{alpha.hat}] the optimal quantile of the \code{s} values. If 
\eqn{s_0=0}{s0=0}, \code{alpha.hat} will not be returned
\item[\code{vec.cv}] the vector of the coefficients of variations. 
Following Tusher et al. (2001), the optimal \code{alpha} quantile 
is given by the quantile that leads to the smallest CV of the
modified test statistics
\item[\code{msg}] a character string summarizing the most important 
information about the fudge factor
\end{ldescription}
\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}},\code{\LinkA{sam.dstat}{sam.dstat}}
\end{SeeAlso}