\HeaderA{assessSpikeIn}{Assessment functions for Spike In Data}{assessSpikeIn}
\aliasA{assessFC}{assessSpikeIn}{assessFC}
\aliasA{assessFC2}{assessSpikeIn}{assessFC2}
\aliasA{assessMA}{assessSpikeIn}{assessMA}
\aliasA{assessSignal}{assessSpikeIn}{assessSignal}
\keyword{manip}{assessSpikeIn}
\begin{Description}\relax
These functions are assessment functoions.
Each takes an
\code{\LinkA{exprSet-class}{exprSet.Rdash.class}} and returns a list with necessary
information to create assessment plots.
\end{Description}
\begin{Usage}
\begin{verbatim}
assessSpikeIn(s,method.name=NULL,verbose=TRUE)

assessMA(exprset,method.name=NULL)
assessSignal(exprset,method.name=NULL)
assessFC(exprset,method.name=NULL)
assessFC2(exprset,method.name=NULL)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{s}] An \code{\LinkA{exprSet-class}{exprSet.Rdash.class}} containing
exrpession measures for 
Affymetrix's spike-in experiment.
\item[\code{exprset}] An \code{\LinkA{exprSet-class}{exprSet.Rdash.class}} containing
exrpession measures for 
Affymetrix's spike-in experiment.
\item[\code{method.name}] Name of expression measure being assessed.
\item[\code{verbose}] logical. If \code{TRUE} show messages.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{assessMA} performs the assessment for the MA-plot (Figure 1),
\code{assessSignal} performs the assessment for signal detection plot
(Figure 4a), \code{assessFC} perfomrs assessments used by fold-change
related  plots (Figures 5a, 6a, 6b). \code{assessFC2} is for the ROC
for genes with nominal fold changes of 2 (Figure
5b). \code{assessSpikeIn} is a wrapper for all these and returns a list
of lists.
\end{Details}
\begin{Value}
Lists with the necessary information to make the Figures.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}

