\HeaderA{scaleParameterPlot}{Scale parameter plotted against mean intensity}{scaleParameterPlot}
\keyword{univar}{scaleParameterPlot}
\keyword{manip}{scaleParameterPlot}
\begin{Description}\relax
Will produce a scatter plot of variance estimators (logged) for each probe (probe set) against the corresponding mean intensity
together with the fitted scale-parameter curve and points showing the knots of the used spline.
\end{Description}
\begin{Usage}
\begin{verbatim}
scaleParameterPlot(model,main="Scale parameter curve",
           col=1,pch='.',lty=1,curveCol=2,knotsPch=19,knotsCol=3)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{model}] On object obtained from the function plw or lmw.
\item[\code{main}] Main title of plot.
\item[\code{col}] Color for individual points (mean,logs2).
\item[\code{pch}] Plot symbol for individual points (mean,logs2).
\item[\code{lty}] Line type for fitted scale parameter curve.
\item[\code{curveCol}] Line color for fitted scale parameter curve.
\item[\code{knotsPch}] Plot symbol for spline knots.
\item[\code{knotsCol}] Plot color for spline knots.
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Magnus \eqn{\mbox{\AA}}{}strand
\end{Author}
\begin{SeeAlso}\relax
plw, lmw
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

# ------------------------------------------
# Example using the result of the analysis of
# the 6 arrays in the AffySpikeU95Subset data set

# Loading the data
data(AffySpikeU95Subset)

# Defining design and contrast matrix
group<-factor(rep(1:2,each=3))
design<-model.matrix(~group-1)
contrast<-matrix(c(1,-1),1,2)

# Analyzing using plw
model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
            epsilon=0.01)

## Look at fitted curve for scale parameter
scaleParameterPlot(model1)

\end{ExampleCode}
\end{Examples}

