\HeaderA{maTwoSamples}{Changing signs for two sample analysis}{maTwoSamples}
\aliasA{widget.TwoSamples}{maTwoSamples}{widget.TwoSamples}
\keyword{manip}{maTwoSamples}
\begin{Description}\relax
Taking target file information and flip the dye swaps experiments.
\end{Description}
\begin{Usage}
\begin{verbatim}
maTwoSamples(targetfile, normdata, Trt, Ctl, targetID = "TargetName", slidesID = "Slides", dyesID = "Dyes", RedID = 5, path = ".", output = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{targetfile}] A data.frame containing target samples information.
\item[\code{normdata}] A R object of class 'marrayNorm'
\item[\code{Trt}] A character string representing "treatment" sample.
\item[\code{Ctl}] A character string representing "controls" sample.
\item[\code{targetID}] A character string representing the column name
in 'targetfile' containing target samples information.
\item[\code{slidesID}] A character string representing the column name
in 'targetfile' containing the slide label.
\item[\code{dyesID}] A character string representing the column name
in 'targetfile' containing dye labeled information.
\item[\code{RedID}] The character use to represent the Cy5 dye.
\item[\code{path}] A character string representing the data directory. By
default this is set to the current working directory ("."). 
\item[\code{output}] Save and tab delimited file
\end{ldescription}
\end{Arguments}
\begin{Value}
An objects of 'marrayNorm' with the dye assignment adjusted.
\end{Value}
\begin{Author}\relax
Yee Hwa (Jean) Yang
\end{Author}