\HeaderA{checkTargetInfo}{Verifying the order between intensities matrix and target file information}{checkTargetInfo}
\keyword{file}{checkTargetInfo}
\begin{Description}\relax
Check that the foreground and backgruond intensities are stored in the
same order as provided in the first column of target file.
\end{Description}
\begin{Usage}
\begin{verbatim}
checkTargetInfo(mraw)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mraw}] Object of class \code{marrayRaw} or \code{marryNorm}.
\end{ldescription}
\end{Arguments}
\begin{Value}
A logical value.  This function returns "TRUE" if the first column from
the Target information is the same order as the foreground and
backgruond intensities.
\end{Value}
\begin{Author}\relax
Yee Hwa (Jean) Yang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
datadir <- system.file("swirldata", package="marray")
swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))
data(swirl)
swirl@maTargets <- swirl.targets

checkTargetInfo(swirl)

checkTargetInfo(swirl[, 2:4])

## reorder
swirl@maTargets <- swirl.targets[c(2:4, 1),]
checkTargetInfo(swirl)
\end{ExampleCode}
\end{Examples}