\HeaderA{getControlData}{Get control probe information}{getControlData}
\keyword{methods}{getControlData}
\begin{Description}\relax
Get control probe information from Bead Studio output or a LumiBatch object.
\end{Description}
\begin{Usage}
\begin{verbatim}
getControlData(x, type = c('data.frame', 'LumiBatch'), ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] the control data can be a LumiBatch object or the Control Probe Profile file outputted by BeadStudio 
\item[\code{type}] determine the return data type 
\item[\code{...}] other parameters used by \code{\LinkA{lumiR}{lumiR}} function 
\end{ldescription}
\end{Arguments}
\begin{Value}
By default, it returns a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the expression amplitudes for individual samples. When type is 'LumiBatch', it returns a LumiBatch object, which basically is the return of lumiR without combining duplicated TargetIDs. As the return is a LumiBatch object, it includes more information, like probe number, detection p-value and standard error of the measurement.
\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')
        ## return a data.frame
        controlData <- getControlData(controlFile)
        class(controlData)
        names(controlData)
        
        ## return a LumiBatch object
        controlData <- getControlData(controlFile, type='LumiBatch')
        summary(controlData)
\end{ExampleCode}
\end{Examples}

