\HeaderA{affycomp.compfigs.auxiliary}{Auxiliary functions to create comparitive Figures}{affycomp.compfigs.auxiliary}
\aliasA{affycomp.compfig2}{affycomp.compfigs.auxiliary}{affycomp.compfig2}
\aliasA{affycomp.compfig2b}{affycomp.compfigs.auxiliary}{affycomp.compfig2b}
\aliasA{affycomp.compfig3}{affycomp.compfigs.auxiliary}{affycomp.compfig3}
\aliasA{affycomp.compfig4a}{affycomp.compfigs.auxiliary}{affycomp.compfig4a}
\aliasA{affycomp.compfig4b}{affycomp.compfigs.auxiliary}{affycomp.compfig4b}
\aliasA{affycomp.compfig4c}{affycomp.compfigs.auxiliary}{affycomp.compfig4c}
\aliasA{affycomp.compfig5a}{affycomp.compfigs.auxiliary}{affycomp.compfig5a}
\aliasA{affycomp.compfig5b}{affycomp.compfigs.auxiliary}{affycomp.compfig5b}
\aliasA{affycomp.compfig5c}{affycomp.compfigs.auxiliary}{affycomp.compfig5c}
\aliasA{affycomp.compfig5cde}{affycomp.compfigs.auxiliary}{affycomp.compfig5cde}
\aliasA{affycomp.compfig5d}{affycomp.compfigs.auxiliary}{affycomp.compfig5d}
\aliasA{affycomp.compfig5e}{affycomp.compfigs.auxiliary}{affycomp.compfig5e}
\keyword{hplot}{affycomp.compfigs.auxiliary}
\begin{Description}\relax
These functions are auxiliary function to
\code{\LinkA{affycompPlot}{affycompPlot}}. These Figures are used to compare
expression measures. They take lists with components created by the
\code{\LinkA{assessDilution}{assessDilution}} and \code{\LinkA{assessSpikeIn}{assessSpikeIn}}
functions.
\end{Description}
\begin{Usage}
\begin{verbatim}
affycomp.compfig2(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 2")

affycomp.compfig3(l, method.names = as.character(1:length(l)),
                  main = "Figure 3")

affycomp.compfig4a(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4a")

affycomp.compfig4b(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, main = "Figure 4b")

affycomp.compfig4c(l, method.names = as.character(1:length(l)),
                   add.legend = TRUE, rotate=TRUE, main = "Figure 4c")

affycomp.compfig5a(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5a", maxfp=100)

affycomp.compfig5b(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5b", maxfp=100)

affycomp.compfig5cde(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100,
                  type=c("low","med","high"))

affycomp.compfig5c(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5c", maxfp=100)

affycomp.compfig5d(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5d", maxfp=100)

affycomp.compfig5e(l, method.names = as.character(1:length(l)),
                  add.legend = TRUE, main = "Figure 5e", maxfp=100)

\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{add.legend}] logical. If TRUE a legend is added.
\item[\code{main}] title of the Figure.
\item[\code{rotate}] in the case of compfig4c one can eiher show the actual
local slopes or the bias (local slope minus 1).
\item[\code{maxfp}] range of the false positives in ROC will be from 0 to \code{maxfp}
\item[\code{type}] compfig5cdef is the engine for 5c, 5d, and
5e. \code{type} tells is which of these 4 to run.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
These are similar to the functions defined in
\code{\LinkA{affycomp.figures.auxiliary}{affycomp.figures.auxiliary}}. Main difference is that
here you send lists with the result of the assessment functions as
components.
\end{Details}
\begin{Value}
Figures are produced.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(rma.assessment)
data(mas5.assessment)
affycomp.compfig2(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig3(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig4a(list(rma.assessment$Signal,mas5.assessment$Signal))
affycomp.compfig4b(list(rma.assessment$Dilution,mas5.assessment$Dilution))
affycomp.compfig5a(list(rma.assessment$FC,mas5.assessment$FC))
affycomp.compfig5b(list(rma.assessment$FC2,mas5.assessment$FC2))
\end{ExampleCode}
\end{Examples}

