\HeaderA{deds.genExtra}{Generating Extra Parameters for Test Statistics Functions for
Differential Expression}{deds.genExtra}
\keyword{manip}{deds.genExtra}
\begin{Description}\relax
\code{deds.genExtra} is used to pass in extra arguments for
\code{\LinkA{comp.stat}{comp.stat}} and \code{\LinkA{deds.stat.linkC}{deds.stat.linkC}},
which computes various test statistics for differential expression
in microarray data.
\end{Description}
\begin{Usage}
\begin{verbatim}
deds.genExtra(classlabel, tests)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{classlabel}] A vector of integers corresponding to observation (column)
class labels. For \eqn{k}{} classes, the labels must be integers
between 0 and \eqn{k-1}{}.
\item[\code{tests}] A vector of character string specifying the statistics to be
used to test differential expression. The character string could be
any of the followings: \\
\Tabular{ll}{
\code{test="t"}: & one- or two-sample t-statistics; \\
\code{test="f"}: & F-statistics;\\
\code{test="fc"}: & fold changes among classes;\\
\code{test="sam"}: & SAM-statistics; \\
\code{test="modt"}: & moderated t-statistics; \\
\code{test="modf"}: & moderated F-statistics; \\
\code{test="B"}: & B-statistics.}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Given the names of the test statistics, \code{deds.genExtra} generates
extra parameters needed to be passed in the functions
\code{comp.stat} and \code{deds.stat.linkC} for the assessment of
differential expression. Both functions are interfaces to C functions.
\code{deds.genExtra} generates default parameters as follows: \\
If \code{test="t" or "f", "fc", "modt", "modf"}, the extra parameter
needed is the number of classes; \\
If \code{test="sam"}, the extra parameter needed is the percentile of
within-gene standard deviations that the fudge factor \eqn{s_0}{} will
be set at and the default is 0.5; \\
If \code{test="B"}, the extra parameter needed is the percentage of
alternative hypotheses (differential expression) and the default is
set at 0.01.
\end{Details}
\begin{Value}
A numeric vector, the length of which is determined by the length of
the names of the test statistics for the argument \code{test}.
\end{Value}
\begin{Author}\relax
Yuanyuan Xiao, \email{yxiao@itsa.ucsf.edu}, \\
Jean Yee Hwa Yang, \email{jean@biostat.ucsf.edu}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{comp.stat}{comp.stat}}, \code{\LinkA{deds.stat.linkC}{deds.stat.linkC}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## two sample test
L <- rep(0:1, c(5,5))
extras <- deds.genExtra(L, c("t","sam", "B"))
## extras will be c(2, 0.5, 0.01)
\end{ExampleCode}
\end{Examples}

