\HeaderA{assessAll}{Assessment functions}{assessAll}
\aliasA{affycomp}{assessAll}{affycomp}
\keyword{manip}{assessAll}
\begin{Description}\relax
Assessment functions.
Takes a couple of 
\code{\LinkA{exprSet-class}{exprSet.Rdash.class}}, one for spike in another for the
dilution and returns a list with necessary
information to create assessment plots.
\end{Description}
\begin{Usage}
\begin{verbatim}
assessAll(d,s,method.name=NULL,verbose=TRUE)

affycomp(d,s,method.name=NULL,verbose=TRUE,return.it=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{d}] An \code{\LinkA{exprSet-class}{exprSet.Rdash.class}} containing
the exrpession measures for the Gene Logic's dilution experiment.
\item[\code{s}] An \code{\LinkA{exprSet-class}{exprSet.Rdash.class}} containing
expression measures for the 
Affymetrix's spike-in experiment.
\item[\code{method.name}] Name of expression measure being assessed.
\item[\code{verbose}] verbosity flag.
\item[\code{return.it}] if \code{TRUE} returns assessment lists.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{assessAll} performs assessments for Figures 1-6. It is a wrapper
for \code{assessDilution} and \code{assessSpikeIn}.

\code{affycomp} is a wrapper that does it all... including the plottitng
and creation of table.
\end{Details}
\begin{Value}
Lists with the necessary information to make the Figures.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}

