\HeaderA{SD}{SD Assessment Functions}{SD}
\aliasA{affycomp.compfig7}{SD}{affycomp.compfig7}
\aliasA{affycomp.figure7}{SD}{affycomp.figure7}
\aliasA{tableSD}{SD}{tableSD}
\keyword{manip}{SD}
\begin{Description}\relax
These functions create assessments, figures, and tables for expression
standard errors
\end{Description}
\begin{Usage}
\begin{verbatim}
affycomp.figure7(l,main="Figure 7")
affycomp.compfig7(l,method.names=as.character(1:length(l)),
                  main="Figure 7")
tableSD(l,method.names=NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{l}] a list of lists with the necessary components to create the
Figure. See details.
\item[\code{method.names}] a character vector with the names of the
expression measures methodologies being compared. 
\item[\code{main}] title of the Figure.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This uses the dilution data. The exprsets need to have standard error
estimates in the \code{se.exprs} slot. Read the vignette for more
details. The functions work similarly to those assessing expression
measures.

All these files need the result of \code{\LinkA{assessSD}{assessSD}}
\end{Details}
\begin{Value}
Depends on the call.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(rma.sd.assessment) ##this was produced with affycomp.assess
data(lw.sd.assessment) ##this one too
affycomp.compfig7(list(rma.sd.assessment,lw.sd.assessment))
affycomp.figure7(rma.sd.assessment)
\end{ExampleCode}
\end{Examples}

