\Header{marrayTwo-class}{Class "marrayTwo", classes and methods for microarray spot statistics}
\alias{maControls,marrayTwo-method}{marrayTwo-class}
\alias{maControls<-,marrayTwo-method}{marrayTwo-class}
\alias{maGridCol,marrayTwo-method}{marrayTwo-class}
\alias{maGridRow,marrayTwo-method}{marrayTwo-class}
\alias{maLayout,marrayTwo-method}{marrayTwo-class}
\alias{maNgc,marrayTwo-method}{marrayTwo-class}
\alias{maNgc<-,marrayTwo,numeric-method}{marrayTwo-class}
\alias{maNgr,marrayTwo-method}{marrayTwo-class}
\alias{maNgr<-,marrayTwo,numeric-method}{marrayTwo-class}
\alias{maNsamples,marrayTwo-method}{marrayTwo-class}
\alias{maNsc,marrayTwo-method}{marrayTwo-class}
\alias{maNsc<-,marrayTwo,numeric-method}{marrayTwo-class}
\alias{maNspots,marrayTwo-method}{marrayTwo-class}
\alias{maNspots<-,marrayTwo,numeric-method}{marrayTwo-class}
\alias{maNsr,marrayTwo-method}{marrayTwo-class}
\alias{maNsr<-,marrayTwo,numeric-method}{marrayTwo-class}
\alias{maPlate,marrayTwo-method}{marrayTwo-class}
\alias{maPlate<-,marrayTwo-method}{marrayTwo-class}
\alias{maPrintTip,marrayTwo-method}{marrayTwo-class}
\alias{marrayTwo}{marrayTwo-class}
\alias{maSpotCol,marrayTwo-method}{marrayTwo-class}
\alias{maSpotRow,marrayTwo-method}{marrayTwo-class}
\alias{maSub,marrayTwo-method}{marrayTwo-class}
\alias{maSub<-,marrayTwo-method}{marrayTwo-class}
\alias{maTargets,marrayTwo-method}{marrayTwo-class}
\alias{maX}{marrayTwo-class}
\alias{maX,marrayTwo-method}{marrayTwo-class}
\alias{maX<\Rdash}{marrayTwo-class}
\alias{maX<-,marrayTwo,matrix-method}{marrayTwo-class}
\alias{maY}{marrayTwo-class}
\alias{maY,marrayTwo-method}{marrayTwo-class}
\alias{maY<\Rdash}{marrayTwo-class}
\alias{maY<-,marrayTwo,matrix-method}{marrayTwo-class}
\alias{print,marrayTwo-method}{marrayTwo-class}
\alias{show,marrayTwo-method}{marrayTwo-class}
\alias{[,marrayTwo-method}{marrayTwo-class}
\keyword{classes}{marrayTwo-class}
\begin{Description}\relax
This class represents pre- or post-normalization intensity data for a batch of cDNA microarrays. A \emph{batch of arrays} consists of a collection of arrays with the same layout  (\code{"\Link{marrayLayout}"}). The class contains slots for two types of spot statistics (e.g. the raw green (Cy3) and red (Cy5) foreground  intensities, or normalized log-ratios M and average intensities A), the layout of the arrays, and a description of the target samples hybridized to the arrays
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form 
\code{  new('marrayRaw',}\\
\code{    maX      = ...., \# Object of class matrix}\\
\code{    maY      = ...., \# Object of class matrix}\\
\code{    maLayout  = ...., \# Object of class marrayLayout}\\
\code{    maTargets = ...., \# Object of class marrayInfo}\\
\code{  )}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{maX}:] Object of class \code{"matrix"}, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maY}:] Object of class \code{"matrix"}, any spot statistic, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maLayout}:] Object of class \code{"\Link{marrayLayout}"},  layout parameters for the cDNA microarrays.
\item[\code{maTargets}:] Object of class \code{"\Link{marrayInfo}"}, description of target samples hybridized to the arrays.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "marrayTwo")}: subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
\item[maControls] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maControls<-] \code{signature(object = "marrayTwo")}:  slot assignment method. 
\item[maGridCol] \code{signature(object = "marrayTwo")}:  method which computes a vector of grid column coordinates for each spot.
\item[maGridRow] \code{signature(object = "marrayTwo")}: method which computes a vector of grid row coordinates for each spot.
\item[maLayout] \code{signature(object = "marrayTwo")}:  slot accessor method.
\item[maLayout<-] \code{signature(object = "marrayTwo", value = "marrayLayout")}: slot assignment method. 
\item[maNgc] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNgc<-] \code{signature(object = "marrayTwo", value = "numeric")}: slot assignment method. 
\item[maNgr] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNgr<-] \code{signature(object = "marrayTwo", value = "numeric")}: slot assignment method. 
\item[maNsamples] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNsc] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNsc<-] \code{signature(object = "marrayTwo", value = "numeric")}: slot assignment method. 
\item[maNspots] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNspots<-] \code{signature(object = "marrayTwo", value = "numeric")}: slot assignment method. 
\item[maNsr] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maNsr<-] \code{signature(object = "marrayTwo", value = "numeric")}: slot assignment method. 
\item[maPlate] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maPlate<-] \code{signature(object = "marrayTwo")}: slot assignment method. 
\item[maPrintTip] \code{signature(object = "marrayTwo")}: method which computes a vector of print-tip-group indices for each spot.
\item[maSpotCol] \code{signature(object = "marrayTwo")}: method which computes a vector of spot column coordinates for each spot.
\item[maSpotRow] \code{signature(object = "marrayTwo")}: method which computes a vector of spot row coordinates for each spot.
\item[maSub] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maSub<-] \code{signature(object = "marrayTwo")}: slot assignment method. 
\item[maTargets] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maTargets<-] \code{signature(object = "marrayTwo", value = "marrayInfo")}: slot assignment method. 
\item[maX] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maX<-] \code{signature(object = "marrayTwo", value = "matrix")}: slot assignment method. 
\item[maY] \code{signature(object = "marrayTwo")}: slot accessor method.
\item[maY<-] \code{signature(object = "marrayTwo", value = "matrix")}: slot assignment method. 
\item[print] \code{signature(x = "marrayTwo")}: print method for \code{"\Link{marrayTwo}"} class.
}
\end{Section}
\begin{Author}\relax
Sandrine Dudoit, \url{http://www.stat.berkeley.edu/~sandrine}.
\end{Author}
\begin{References}\relax
S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, \emph{The Analysis of Gene Expression Data: Methods and Software}, Springer, New York.
\end{References}
\begin{SeeAlso}\relax
\code{\Link{marrayLayout}}, \code{\Link{marrayRaw}}, \code{\Link{marrayNorm}}, \code{\Link{marrayInfo}}, \code{\Link{marraySpots}}, \code{\Link{print-methods}}, \code{\Link{[-methods}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## See marrayRaw
\end{ExampleCode}
\end{Examples}

