\HeaderA{assessSpikeIn2}{New Assessment functions for Spike In Data}{assessSpikeIn2}
\aliasA{assessLS}{assessSpikeIn2}{assessLS}
\aliasA{assessMA2}{assessSpikeIn2}{assessMA2}
\aliasA{assessSpikeInSD}{assessSpikeIn2}{assessSpikeInSD}
\keyword{manip}{assessSpikeIn2}
\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}
assessSpikeIn2(s,method.name=NULL,verbose=TRUE)

assessSpikeInSD(exprset,method.name=NULL,span=1/3)
assessLS(exprset,method.name=NULL)
assessMA2(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.
\item[\code{span}] span used in call to \code{loess}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{assessMA2} performs the assessment for the second MA-plot (Figure 1b),
\code{assessLS} performs the assessment for signal detection plot
(Figure 4c), \code{assessMA2} also perfomrs assessments used by
fold-change related  plots (Figures 5c-f). \code{assessSpikeInSD} is
for the standard deviation assessment of Figure 2b.
\code{assessSpikeIn2} 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}

