\HeaderA{affycompTable}{Expression Assessment Table}{affycompTable}
\aliasA{tableAll}{affycompTable}{tableAll}
\aliasA{tableDilution}{affycompTable}{tableDilution}
\aliasA{tableFC}{affycompTable}{tableFC}
\aliasA{tableFC2}{affycompTable}{tableFC2}
\aliasA{tableLS}{affycompTable}{tableLS}
\aliasA{tableMA2}{affycompTable}{tableMA2}
\aliasA{tableOverallSNR}{affycompTable}{tableOverallSNR}
\aliasA{tableRanks}{affycompTable}{tableRanks}
\aliasA{tableSignal}{affycompTable}{tableSignal}
\aliasA{tableSpikeInSD}{affycompTable}{tableSpikeInSD}
\keyword{manip}{affycompTable}
\begin{Description}\relax
These functions takes as an argument the output of the asessment
functions.
\end{Description}
\begin{Usage}
\begin{verbatim}
affycompTable(...,Table=NULL,assessment.list=NULL,method.names=NULL)

tableAll(...,assessment.list=NULL,method.names=NULL)

tableDilution(l, method.names=NULL)

tableFC(l, method.names=NULL)

tableFC2(l, method.names=NULL)

tableSignal(l, method.names=NULL)

tableLS(l, method.names=NULL)

tableSpikeInSD(l, method.names=NULL)

tableMA2(l, method.names=NULL)

tableOverallSNR(...,assessment.list=NULL,method.names=NULL,ngenes=12626)

tableRanks(...,assessment.list=NULL,method.names=NULL,ngenes=12626,rank=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{...}] lists produced by the assessment functions
\item[\code{Table}] If \code{TableAll} was used one can send it through this argument
\item[\code{assessment.list}] Alternatively, one can also send a list of lists produced by \code{\LinkA{tableAll}{tableAll}}.
\item[\code{method.names}] A character vector with the names of the
epxression measure methodology.
\item[\code{l}] list of assessments.
\item[\code{rank}] if \code{TRUE} \code{tableRanks} will present ranks instead
of local slopes.
\item[\code{ngenes}] when computing ranks, out of how many genes should we do it?
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Read the vignette for more details on what the entries of the table
are. \code{affycompTable} has a few entries per graph. \code{tableAll}
has more entries. Once an
assessment is used this function knows what to do. You can call any of
the assessment functions described in \code{\LinkA{assessSpikeIn}{assessSpikeIn}},
\code{\LinkA{assessDilution}{assessDilution}}, \code{\LinkA{assessSD}{assessSD}},
\code{\LinkA{assessLS}{assessLS}}, \code{\LinkA{assessMA2}{assessMA2}}, and \code{\LinkA{assessSpikeInSD}{assessSpikeInSD}}.

Note \code{tableRanks} and \code{tableOverallSNR} work on the results
from \code{\LinkA{assessSpikeIn2}{assessSpikeIn2}}.
\end{Details}
\begin{Value}
A matrix. One column per each method and one row for each comparison.
tableOverallSNR is an exception. Where rows represnt methods.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(rma.assessment) ##this was produced with affycomp.assess
data(mas5.assessment) ##this one too
tmp <- affycompTable(mas5.assessment,rma.assessment)
format(tmp,digit=2)
\end{ExampleCode}
\end{Examples}

