\HeaderA{plotControlData}{Plot the mean expression (with standard deviation bar) of different type of control probes}{plotControlData}
\keyword{methods}{plotControlData}
\keyword{hplot}{plotControlData}
\begin{Description}\relax
Plot the mean expression (with standard deviation bar) of different type of control probes. Multiple control types can be plotted in a single plot. The available control types can be get by running getControlType(controlData).
\end{Description}
\begin{Usage}
\begin{verbatim}
plotControlData(controlData, type = NULL, slideIndex = NULL, logMode = FALSE, new = TRUE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{controlData}] a LumiBatch object including control data or a control data data.frame
\item[\code{type}] the control probe type (case insensitive), which can be get by running getControlType(controlData) 
\item[\code{slideIndex}] the slide index or ID corresponding to each sample 
\item[\code{logMode}] whether show the data in log2 scale 
\item[\code{new}] whether refresh the new plot or add it on the old one  
\item[\code{...}] other parameters used by default plot function 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
When multiple control types are selected, they will be plotted in a two-column plot.
\end{Details}
\begin{Value}
plot the picture and return TRUE if everything is OK
\end{Value}
\begin{Author}\relax
Pan Du
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{addControlData2lumi}{addControlData2lumi}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        controlFile <- system.file('doc', 'Control_Probe_Profile.txt', package='lumi')
        controlData <- getControlData(controlFile)
        getControlType(controlData)
        plotControlData(controlData, type='NEGATIVE')
\end{ExampleCode}
\end{Examples}

