\Header{marrayNorm-class}{Class "marrayNorm", classes and methods for post-normalization cDNA microarray intensity data}
\alias{cbind,marrayNorm-method}{marrayNorm-class}
\alias{coerce,marrayNorm,exprSet-method}{marrayNorm-class}
\alias{coerce,marrayNorm,marraySpots-method}{marrayNorm-class}
\alias{coerce,marrayRaw,marrayNorm-method}{marrayNorm-class}
\alias{maA}{marrayNorm-class}
\alias{maA,marrayNorm-method}{marrayNorm-class}
\alias{maA<\Rdash}{marrayNorm-class}
\alias{maA<-,marrayNorm,matrix-method}{marrayNorm-class}
\alias{maControls,marrayNorm-method}{marrayNorm-class}
\alias{maControls<-,marrayNorm-method}{marrayNorm-class}
\alias{maGnames,marrayNorm-method}{marrayNorm-class}
\alias{maGridCol,marrayNorm-method}{marrayNorm-class}
\alias{maGridRow,marrayNorm-method}{marrayNorm-class}
\alias{maLayout,marrayNorm-method}{marrayNorm-class}
\alias{maM}{marrayNorm-class}
\alias{maM,marrayNorm-method}{marrayNorm-class}
\alias{maM<\Rdash}{marrayNorm-class}
\alias{maM<-,marrayNorm,matrix-method}{marrayNorm-class}
\alias{maMloc}{marrayNorm-class}
\alias{maMloc,marrayNorm-method}{marrayNorm-class}
\alias{maMloc<\Rdash}{marrayNorm-class}
\alias{maMloc<-,marrayNorm,matrix-method}{marrayNorm-class}
\alias{maMscale}{marrayNorm-class}
\alias{maMscale,marrayNorm-method}{marrayNorm-class}
\alias{maMscale<\Rdash}{marrayNorm-class}
\alias{maMscale<-,marrayNorm,matrix-method}{marrayNorm-class}
\alias{maNgc,marrayNorm-method}{marrayNorm-class}
\alias{maNgc<-,marrayNorm,numeric-method}{marrayNorm-class}
\alias{maNgr,marrayNorm-method}{marrayNorm-class}
\alias{maNgr<-,marrayNorm,numeric-method}{marrayNorm-class}
\alias{maNormCall}{marrayNorm-class}
\alias{maNormCall,marrayNorm-method}{marrayNorm-class}
\alias{maNotes,marrayNorm-method}{marrayNorm-class}
\alias{maNotes<-,marrayNorm,character-method}{marrayNorm-class}
\alias{maNsamples,marrayNorm-method}{marrayNorm-class}
\alias{maNsc,marrayNorm-method}{marrayNorm-class}
\alias{maNsc<-,marrayNorm,numeric-method}{marrayNorm-class}
\alias{maNspots,marrayNorm-method}{marrayNorm-class}
\alias{maNspots<-,marrayNorm,numeric-method}{marrayNorm-class}
\alias{maNsr,marrayNorm-method}{marrayNorm-class}
\alias{maNsr<-,marrayNorm,numeric-method}{marrayNorm-class}
\alias{maPlate,marrayNorm-method}{marrayNorm-class}
\alias{maPlate<-,marrayNorm-method}{marrayNorm-class}
\alias{maPrintTip,marrayNorm-method}{marrayNorm-class}
\alias{marrayNorm}{marrayNorm-class}
\alias{maSpotCol,marrayNorm-method}{marrayNorm-class}
\alias{maSpotRow,marrayNorm-method}{marrayNorm-class}
\alias{maSub,marrayNorm-method}{marrayNorm-class}
\alias{maSub<-,marrayNorm-method}{marrayNorm-class}
\alias{maTargets,marrayNorm-method}{marrayNorm-class}
\alias{maW,marrayNorm-method}{marrayNorm-class}
\alias{maW<-,marrayNorm,matrix-method}{marrayNorm-class}
\alias{print,marrayNorm-method}{marrayNorm-class}
\alias{show,marrayNorm-method}{marrayNorm-class}
\alias{[,marrayNorm-method}{marrayNorm-class}
\keyword{classes}{marrayNorm-class}
\begin{Description}\relax
This class represents 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 the average log-intensities A, the normalized log-ratios M, the location and scale normalization values, the layout of the arrays, and descriptions of the target samples hybridized to the arrays and 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('marrayNorm',}\\
\code{    maA        = ...., \# Object of class matrix}\\
\code{    maM        = ...., \# Object of class matrix}\\
\code{    maMloc     = ...., \# Object of class matrix}\\
\code{    maMscale   = ...., \# Object of class matrix}\\
\code{    maW        = ...., \# Object of class matrix}\\
\code{    maLayout   = ...., \# Object of class marrayLayout}\\
\code{    maGnames   = ...., \# Object of class marrayInfo}\\
\code{    maTargets  = ...., \# Object of class marrayInfo}\\
\code{    maNotes    = ...., \# Object of class character}\\
\code{    maNormCall = ...., \# Object of class call}\\
\code{  )}\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{maA}:] Object of class \code{"matrix"}, average log-intensities (base 2) A, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maM}:] Object of class \code{"matrix"}, intensity log-ratios (base 2) M, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maMloc}:] Object of class \code{"matrix"}, location normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maMscale}:] Object of class \code{"matrix"},  scale normalization values, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maW}:] Object of class \code{"matrix"}, spot quality weights, rows correspond to spotted probe sequences, columns to arrays in the batch.
\item[\code{maLayout}:] Object of class \code{"\Link{marrayLayout}"}, layout parameters for cDNA microarrays.
\item[\code{maGnames}:] Object of class \code{"\Link{marrayInfo}"}, description of spotted probe sequences.
\item[\code{maTargets}:] Object of class \code{"\Link{marrayInfo}"}, description of target samples hybridized to the arrays.
\item[\code{maNotes}:] Object of class \code{"character"}, any notes concerning the microarray experiments, e.g. hybridization or scanning conditions.
\item[\code{maNormCall}:] Object of class \code{"call"}, function call for normalizing the batch of arrays.
}\end{Section}
\begin{Section}{Methods}
\describe{
\item[[] \code{signature(x = "marrayNorm")}:  subsetting operator for spots on the array and arrays in the batch, ensures that all slots are subset properly.
\item[coerce] \code{signature(from = "marrayRaw", to = "marrayNorm")}: coerce an object of class \code{"\Link{marrayRaw}"} into an object of class \code{\Link{marrayNorm}}. 
\item[coerce] \code{signature(from = "marrayNorm", to = "exprSet")}: coerce an object of class \code{"\Link{marrayNorm}"} into an object of class \code{\Link{exprSet-class}}. 
\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[maA] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maA<-] \code{signature(object = "marrayNorm", value = "matrix")}: slot assignment method. 
\item[maControls<-] \code{signature(object = "marrayNorm")}: slot assignment method. 
\item[maControls] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maGnames] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maGnames<-] \code{signature(object = "marrayNorm", value = "marrayInfo")}: slot assignment method. 
\item[maGridCol] \code{signature(object = "marrayNorm")}: method which computes a vector of grid column coordinates for each spot.
\item[maGridRow] \code{signature(object = "marrayNorm")}: method which computes a vector of grid row coordinates for each spot.
\item[maLayout] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maLayout<-] \code{signature(object = "marrayNorm", value = "marrayLayout")}: slot assignment method. 
\item[maM] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maM<-] \code{signature(object = "marrayNorm", value = "matrix")}: slot assignment method. 
\item[maMloc] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maMloc<-] \code{signature(object = "marrayNorm", value = "matrix")}: slot assignment method. 
\item[maMscale] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maMscale<-] \code{signature(object = "marrayNorm", value = "matrix")}: slot assignment method. 
\item[maNgc] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNgc<-] \code{signature(object = "marrayNorm", value = "numeric")}: slot assignment method. 
\item[maNgr] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNgr<-] \code{signature(object = "marrayNorm", value = "numeric")}: slot assignment method. 
\item[maNormCall] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNotes] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNotes<-] \code{signature(object = "marrayNorm", value = "character")}: slot assignment method. 
\item[maNsamples] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNsc] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNsc<-] \code{signature(object = "marrayNorm", value = "numeric")}: slot assignment method. 
\item[maNspots] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNspots<-] \code{signature(object = "marrayNorm", value = "numeric")}: slot assignment method. 
\item[maNsr] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maNsr<-] \code{signature(object = "marrayNorm", value = "numeric")}: slot assignment method. 
\item[maPlate] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maPlate<-] \code{signature(object = "marrayNorm")}: slot assignment method. 
\item[maPrintTip] \code{signature(object = "marrayNorm")}: method which computes a vector of print-tip-group indices for each spot.
\item[maSpotCol] \code{signature(object = "marrayNorm")}: method which computes a vector of spot column coordinates for each spot.
\item[maSpotRow] \code{signature(object = "marrayNorm")}: method which computes a vector of spot row coordinates for each spot.
\item[maSub] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maSub<-] \code{signature(object = "marrayNorm")}: slot assignment method. 
\item[maTargets] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maTargets<-] \code{signature(object = "marrayNorm", value = "marrayInfo")}: slot assignment method.  
\item[maW] \code{signature(object = "marrayNorm")}: slot accessor method.
\item[maW<-] \code{signature(object = "marrayNorm", value = "matrix")}: slot assignment method. 
\item[print] \code{signature(x = "marrayNorm")}: print method for \code{"\Link{marrayNorm}"} 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{marrayInfo}}, \code{\Link{marraySpots}}, \code{\Link{marrayTwo}}, \code{\Link{exprSet-class}}, \code{\Link{print-methods}}, \code{\Link{[-methods}}, \code{\Link{coerce-methods}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Examples use swirl dataset, for description type ? swirl

# data(swirl)

# Normalization is done using functions from the marrayNorm package
# library(marrayNorm)

# Within-print-tip-group loess location normalization
# mnorm<-maNorm(swirl[,2:3],norm="p")

# Object of class marrayNorm for the second and third swirl arrays
# mnorm

# Function call
# maNormCall(mnorm)

#  Object of class marrayInfo -- Probe sequences
# maGnames(mnorm)

#  Object of class marrayInfo -- Target samples
# maTargets(mnorm)

# Density plot of log-ratios M for third array
# plot(density(maM(mnorm[,2])), lwd=2, col=2, main="Density plots of log-ratios M")
# lines(density(maM(swirl[,3])), lwd=2)
# abline(v=0)
# legend(2,1,c("Pre-normalization","Post-normalization"))

\end{ExampleCode}
\end{Examples}

