\Header{rg.quantarray}{Extract RGList from data.frames Containing Quantarray Data}
\keyword{IO}{rg.quantarray}
\begin{Description}\relax
Extracts an RGList from Quantarray image analysis output when the data has already been read from files into data.frames objects.
\end{Description}
\begin{Usage}
\begin{verbatim}
rg.quantarray(slides,names.slides=names(slides),suffix="qta")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{slides}] Character vector giving the names of the data frames containing the Spot output.
\item[\code{names.slides}] Names to be associated with each slide as column name.
\item[\code{suffix}] The dataframe names are assumed to have this suffix added to names in \code{slides}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function extracts the foreground and background intensities from a series of data frames and assembles them in the components of one list.
\end{Details}
\begin{Value}
A list containing the components
\begin{ldescription}
\item[\code{R}] A matrix containing the red channel foreground intensities for each spot for each array.
\item[\code{Rb}] A matrix containing the red channel background intensities for each spot for each array.
\item[\code{G}] A matrix containing the green channel foreground intensities for each spot for each array.
\item[\code{Gb}] A matrix containing the green channel background intensities for each spot for each array.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of LIMMA functions for reading data is given in \link{3.ReadingData}.
\end{SeeAlso}

