\Header{marraySpots-class}{Class "marraySpots", classes and methods for probe sequences spotted on microarrays}
\alias{maControls,marraySpots-method}{marraySpots-class}
\alias{maControls<-,marraySpots-method}{marraySpots-class}
\alias{maGnames,marraySpots-method}{marraySpots-class}
\alias{maGridCol,marraySpots-method}{marraySpots-class}
\alias{maGridRow,marraySpots-method}{marraySpots-class}
\alias{maLayout,marraySpots-method}{marraySpots-class}
\alias{maNgc,marraySpots-method}{marraySpots-class}
\alias{maNgc<-,marraySpots,numeric-method}{marraySpots-class}
\alias{maNgr,marraySpots-method}{marraySpots-class}
\alias{maNgr<-,marraySpots,numeric-method}{marraySpots-class}
\alias{maNsc,marraySpots-method}{marraySpots-class}
\alias{maNsc<-,marraySpots,numeric-method}{marraySpots-class}
\alias{maNspots,marraySpots-method}{marraySpots-class}
\alias{maNspots<-,marraySpots,numeric-method}{marraySpots-class}
\alias{maNsr,marraySpots-method}{marraySpots-class}
\alias{maNsr<-,marraySpots,numeric-method}{marraySpots-class}
\alias{maPlate,marraySpots-method}{marraySpots-class}
\alias{maPlate<-,marraySpots-method}{marraySpots-class}
\alias{maPrintTip,marraySpots-method}{marraySpots-class}
\alias{marraySpots}{marraySpots-class}
\alias{maSpotCol,marraySpots-method}{marraySpots-class}
\alias{maSpotRow,marraySpots-method}{marraySpots-class}
\alias{maSub,marraySpots-method}{marraySpots-class}
\alias{maSub<-,marraySpots-method}{marraySpots-class}
\alias{print,marraySpots-method}{marraySpots-class}
\alias{show,marraySpots-method}{marraySpots-class}
\alias{[,marraySpots-method}{marraySpots-class}
\keyword{classes}{marraySpots-class}
\begin{Description}\relax
This class stores information on the spotted probe sequences for a batch of arrays.
A \emph{batch of arrays} consists of a collection of arrays with the same layout  (\code{"\Link{marrayLayout}"}). The class contains slots for the layout of the arrays, and a description of the probe sequences spotted onto the arrays.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form 
\code{  new('marraySpots',}\\
\code{    maGnames = ...., \# Object of class marrayInfo}\\
\code{    maLayout  = ...., \# Object of class marrayLayout}\\\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{maGnames}:] Object of class \code{"\Link{marrayInfo}"},  description of spotted probe sequences.
\item[\code{maLayout}:] Object of class \code{"\Link{marrayLayout}"}, layout parameters for the cDNA microarrays.
}\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "marraySpots")}:  subsetting operator for spots on the array, ensures that all slots are subset properly.
\item[coerce] \code{signature(from = "marrayRaw", to = "marraySpots")}: coerce an object of class \code{"\Link{marrayRaw}"} into an object of class \code{"\Link{marraySpots}"}. 
\item[coerce] \code{signature(from = "marrayNorm", to = "marraySpots")}: coerce an object of class \code{"\Link{marrayNorm}"} into an object of class \code{"\Link{marraySpots}"}.  
\item[maControls] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maControls<-] \code{signature(object = "marraySpots")}:  slot assignment method. 
\item[maGnames] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maGnames<-] \code{signature(object = "marraySpots", value = "marrayInfo")}: slot assignment method. 
\item[maGridCol] \code{signature(object = "marraySpots")}:  method which computes a vector of grid column coordinates for each spot.
\item[maGridRow] \code{signature(object = "marraySpots")}: method which computes a vector of grid row coordinates for each spot.
\item[maLayout] \code{signature(object = "marraySpots")}:  slot accessor method.
\item[maLayout<-] \code{signature(object = "marraySpots", value = "marrayLayout")}: slot assignment method. 
\item[maNgc] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maNgc<-] \code{signature(object = "marraySpots", value = "numeric")}: slot assignment method. 
\item[maNgr] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maNgr<-] \code{signature(object = "marraySpots", value = "numeric")}: slot assignment method. 
\item[maNsc] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maNsc<-] \code{signature(object = "marraySpots", value = "numeric")}: slot assignment method. 
\item[maNspots] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maNspots<-] \code{signature(object = "marraySpots", value = "numeric")}: slot assignment method. 
\item[maNsr] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maNsr<-] \code{signature(object = "marraySpots", value = "numeric")}: slot assignment method. 
\item[maPlate] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maPlate<-] \code{signature(object = "marraySpots")}: slot assignment method. 
\item[maPrintTip] \code{signature(object = "marraySpots")}: method which computes a vector of print-tip-group indices for each spot.
\item[maSpotCol] \code{signature(object = "marraySpots")}: method which computes a vector of spot column coordinates for each spot.
\item[maSpotRow] \code{signature(object = "marraySpots")}: method which computes a vector of spot row coordinates for each spot.
\item[maSub] \code{signature(object = "marraySpots")}: slot accessor method.
\item[maSub<-] \code{signature(object = "marraySpots")}: slot assignment method. 
\item[print] \code{signature(x = "marraySpots")}: print method for \code{"\Link{marraySpots}"} 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{marrayTwo}}, \code{\Link{print-methods}}, \code{\Link{[-methods}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## See marrayRaw
\end{ExampleCode}
\end{Examples}

