\HeaderA{plot.t2}{Diagnostic Plots for Two-Sample t-statistics}{plot.t2}
\keyword{hplot}{plot.t2}
\begin{Description}\relax
Plots of two-sample t-statistics, |t-numerator| and
t-denominator against average A, and plot of |t-numerator| against
t-denominator. For each spot on a given slide, \eqn{A = log_2
\sqrt{RG}}{A = log_2(R*G)/2}, where (R,G) denotes the red and green
fluorescence intensity pair. Points with t-statistics exceeding user
defined thresholds are highlighted.
\end{Description}
\begin{Usage}
\begin{verbatim}
plot.t2(x, main.title="T plots", low=-5, high=5,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] output from the function \code{\LinkA{stat.t2}{stat.t2}}.
\item[\code{main.title}] title for the plot.
\item[\code{low}] lower threshold for t-statistic: points with t<low are
colored in green.
\item[\code{high}] upper threshold for t-statistic: points with t>high are
colored in red.
\item[\code{...}] additional graphical parameters
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Sandrine Dudoit, \email{sandrine@stat.berkeley.edu} \\
Yee Hwa Yang, \email{yeehwa@stat.berkeley.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stat.t2}{stat.t2}}, \code{\LinkA{t2stat.func}{t2stat.func}},
\code{\LinkA{plot}{plot}}, \code{\LinkA{t.test}{t.test}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(MouseArray)
# mouse.setup <- init.grid()
# mouse.data <- init.data() ## see \emph{init.data}
# mouse.lratio <- stat.ma(mouse.data, mouse.setup)

## Calculation of t-statistics
## cl <- c(rep(1,3), rep(2,3))
## mouse.t2 <- stat.t2(mouse.lratio, cl)

## Diagnostic plots
plot.t2(mouse.t2, "Mouse")
\end{ExampleCode}
\end{Examples}

