\HeaderA{affycomp.figures.auxiliary}{Auxiliary functions to create Figures}{affycomp.figures.auxiliary}
\aliasA{affycomp.figure1}{affycomp.figures.auxiliary}{affycomp.figure1}
\aliasA{affycomp.figure1b}{affycomp.figures.auxiliary}{affycomp.figure1b}
\aliasA{affycomp.figure2}{affycomp.figures.auxiliary}{affycomp.figure2}
\aliasA{affycomp.figure2b}{affycomp.figures.auxiliary}{affycomp.figure2b}
\aliasA{affycomp.figure3}{affycomp.figures.auxiliary}{affycomp.figure3}
\aliasA{affycomp.figure4a}{affycomp.figures.auxiliary}{affycomp.figure4a}
\aliasA{affycomp.figure4b}{affycomp.figures.auxiliary}{affycomp.figure4b}
\aliasA{affycomp.figure4c}{affycomp.figures.auxiliary}{affycomp.figure4c}
\aliasA{affycomp.figure5a}{affycomp.figures.auxiliary}{affycomp.figure5a}
\aliasA{affycomp.figure5b}{affycomp.figures.auxiliary}{affycomp.figure5b}
\aliasA{affycomp.figure5c}{affycomp.figures.auxiliary}{affycomp.figure5c}
\aliasA{affycomp.figure5d}{affycomp.figures.auxiliary}{affycomp.figure5d}
\aliasA{affycomp.figure5e}{affycomp.figures.auxiliary}{affycomp.figure5e}
\aliasA{affycomp.figure6a}{affycomp.figures.auxiliary}{affycomp.figure6a}
\aliasA{affycomp.figure6b}{affycomp.figures.auxiliary}{affycomp.figure6b}
\keyword{hplot}{affycomp.figures.auxiliary}
\begin{Description}\relax
These functions are auxiliary function to
\code{\LinkA{affycompPlot}{affycompPlot}}. These Figures are used to assess an
expression measure. They take components created by the
\code{\LinkA{assessDilution}{assessDilution}} and \code{\LinkA{assessSpikeIn}{assessSpikeIn}}
functions.
\end{Description}
\begin{Usage}
\begin{verbatim}
affycomp.figure1(l,main="Figure 1",xlim=NULL,ylim=NULL)
affycomp.figure1b(l,main="Figure 1b",xlim=NULL,ylim=NULL,cex=0.85,all=FALSE)
affycomp.figure2(l,main="Figure 2")
affycomp.figure2b(l,main="Figure 2b")
affycomp.figure3(l, main = "Figure 3")
affycomp.figure4a(l, main = "Figure 4a",equal.lims=FALSE)
affycomp.figure4b(l, main = "Figure 4b")
affycomp.figure4c(l, rotate=TRUE, main = "Figure 4c")
affycomp.figure5a(l, main = "Figure 5a",maxfp=100)
affycomp.figure5b(l, main = "Figure 5b",maxfp=100)
affycomp.figure5c(l, main = "Figure 5c",maxfp=100)
affycomp.figure5d(l, main = "Figure 5d",maxfp=100)
affycomp.figure5e(l, main = "Figure 5e",maxfp=100)
affycomp.figure6a(l, main = "Figure 6a",xlim = NULL, ylim = NULL)
affycomp.figure6b(l, main = "Figure 6b",xlim = NULL, ylim = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{l}] A list with the necessary components to create the
Figure. See details.
\item[\code{main}] Title for the Figure.
\item[\code{maxfp}] range of the false positives in ROC will be from 0 to \code{maxfp}
\item[\code{xlim}] x-axis limits.
\item[\code{ylim}] y-axis limits.
\item[\code{cex}] size of numbers in figure 1b.
\item[\code{all}] logical. If \code{TRUE} all spikeins are shown. Otherwise,
only those resulting in smaller, realistic, fold changes are shown.
\item[\code{equal.lims}] logical. If \code{TRUE} the limits of x-axis and
y-axis will have same range.
\item[\code{rotate}] in the case of compfig4c one can eiher show the actual
local slopes or the bias (local slope minus 1).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Read the vignette for more details on what each Figure is. You can read
\code{\LinkA{assessSpikeIn}{assessSpikeIn}} and \code{\LinkA{assessDilution}{assessDilution}} to see
which assessments are needed.
\end{Details}
\begin{Value}
Figures are produced.
\end{Value}
\begin{Author}\relax
Rafael A. Irizarry
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(rma.assessment)
affycomp.figure1(rma.assessment$MA)
affycomp.figure2(rma.assessment$Dilution)
affycomp.figure3(rma.assessment$Dilution)
affycomp.figure4a(rma.assessment$Signal)
affycomp.figure4b(rma.assessment$Dilution)
affycomp.figure5a(rma.assessment$FC)
affycomp.figure5b(rma.assessment$FC2)
affycomp.figure6a(rma.assessment$FC)
affycomp.figure6b(rma.assessment$FC)
\end{ExampleCode}
\end{Examples}

