\Header{AffyBatch-class}{Class AffyBatch}
\alias{\$.AffyBatch}{AffyBatch-class}
\alias{AffyBatch}{AffyBatch-class}
\alias{bg.correct,AffyBatch,character-method}{AffyBatch-class}
\alias{boxplot,AffyBatch-method}{AffyBatch-class}
\alias{cdfName}{AffyBatch-class}
\alias{cdfName,AffyBatch-method}{AffyBatch-class}
\methalias{cdfName,AffyBatch-method}{AffyBatch-class}
\alias{computeExprSet,AffyBatch,character,character-method}{AffyBatch-class}
\alias{geneNames}{AffyBatch-class}
\alias{geneNames,AffyBatch-method}{AffyBatch-class}
\alias{getCdfInfo}{AffyBatch-class}
\alias{getCdfInfo,AffyBatch-method}{AffyBatch-class}
\alias{hist,AffyBatch-method}{AffyBatch-class}
\alias{image}{AffyBatch-class}
\alias{image,AffyBatch-method}{AffyBatch-class}
\alias{indexProbes}{AffyBatch-class}
\alias{indexProbes,AffyBatch,character-method}{AffyBatch-class}
\alias{indexProbes,AffyBatch-method}{AffyBatch-class}
\alias{intensity}{AffyBatch-class}
\alias{intensity,AffyBatch-method}{AffyBatch-class}
\alias{intensity<\Rdash}{AffyBatch-class}
\alias{intensity<-,AffyBatch-method}{AffyBatch-class}
\alias{length,AffyBatch-method}{AffyBatch-class}
\alias{mm,AffyBatch-method}{AffyBatch-class}
\alias{mm<-,AffyBatch,ANY-method}{AffyBatch-class}
\alias{mmindex}{AffyBatch-class}
\alias{mmindex,AffyBatch-method}{AffyBatch-class}
\alias{ncol,AffyBatch-method}{AffyBatch-class}
\alias{nrow,AffyBatch-method}{AffyBatch-class}
\alias{pm,AffyBatch-method}{AffyBatch-class}
\alias{pm<-,AffyBatch,ANY-method}{AffyBatch-class}
\alias{pmindex}{AffyBatch-class}
\alias{pmindex,AffyBatch-method}{AffyBatch-class}
\alias{probeNames,AffyBatch-method}{AffyBatch-class}
\alias{probes}{AffyBatch-class}
\alias{probes,AffyBatch-method}{AffyBatch-class}
\alias{probeset}{AffyBatch-class}
\alias{probeset,AffyBatch-method}{AffyBatch-class}
\alias{show,AffyBatch-method}{AffyBatch-class}
\alias{[,AffyBatch-method}{AffyBatch-class}
\alias{[<-,AffyBatch-method}{AffyBatch-class}
\alias{[[,AffyBatch-method}{AffyBatch-class}
\keyword{classes}{AffyBatch-class}
\begin{Description}\relax
This is a class representation for Affymetrix GeneChip probe
level data. The main component are the intensities from multiple
arrays of the same \code{CDF} type. In extends \code{\Link{exprSet-class}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created using the function \code{\Link{read.affybatch}}
or the wrapper \code{\Link{ReadAffy}}.\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{cdfName}:] Object of class \code{"character"} representing the name of
\code{CDF} file associated with the arrays in the \code{AffyBatch}.
\item[\code{nrow}:] Object of class \code{"numeric"} representing
the physical number of rows in the arrays.
\item[\code{ncol}:] Object of class \code{"numeric"} representing
the physical number of columns in the arrays.
\item[\code{exprs}:] Object of class "matrix" inherited from
\code{exprSet}. The matrix contains one probe per row and one chip
per column.
\item[\code{se.exprs}:] Object of class "matrix" inherited from \code{exprSet}.
\item[\code{phenoData}:] Object of class "phenoData" inherited from
\code{exprSet}.
\item[\code{annotation}] A character string identifying the
annotation that may be used for the \code{exprSet} instance.
\item[\code{description}:] Object of class "MIAME". For
compatibility with previous version of this class description can
also be a "character". The class \code{characterOrMIAME} has been
defined just for this. 
\item[\code{notes}:] Object of class "character" Vector of
explanatory text 
}\end{Section}
\begin{Section}{Extends}
Class \code{"exprSet"}, directly.\end{Section}
\begin{Section}{Methods}
\describe{
\item[cdfName] \code{signature(object = "AffyBatch")}: Obtains the
cdfName slot.
\item[pm<-] \code{signature(object = "AffyBatch")}: replaces the
perfect match intensities 
\item[pm] \code{signature(object = "AffyBatch")}: extracts the pm intensities. 
\item[mm<-] \code{signature(object = "AffyBatch")}: replaces the
mismatch intensities.
\item[mm] \code{signature(object = "AffyBatch")}: extracts the mm intensities. 
\item[probes] \code{signature(object = "AffyBatch", which)}: extract the
perfect match or mismatch probe intensities. Uses which can be "pm"
and "mm".
\item[[<-] \code{signature(x = "AffyBatch")}: replaces subsets. 
\item[[] \code{signature(x = "AffyBatch")}: subsets by array.
\item[[[] \code{signature(x = "AffyBatch")}: extracts each array as
an \code{\Link{Cel}} instance.
\item[boxplot] \code{signature(x = "AffyBatch")}:  creates a
\code{\Link{boxplot}s of log base 2 intensities. }
\item[hist] \code{signature(x = "AffyBatch")}:  creates a
plot showing all the histograms of the pm,mm or both data. See
\code{\Link{plot.density}}
\item[computeExprSet] \code{signature(x = "AffyBatch",
        summary.method = "character")}: For each probe set computes an
expression value using \code{summary.method}. 
\item[geneNames] \code{signature(object = "AffyBatch")}: return the
probe set names also referred to as the Affymetrix IDs. 
\item[getCdfInfo] \code{signature(object = "AffyBatch")}: retrieve
the environment that defines the location of probes by probe set. 
\item[image] \code{signature(x = "AffyBatch")}: creates an image for
each sample.
\item[indexProbes] \code{signature(object = "AffyBatch", which =
        "character")}: returns a list with locations of the probes in
each probe set. The affyID corresponding to the probe set to
retrieve can be specified in an optional parameter
\code{genenames}. By default, all the affyIDs are retrieved.
The names of the elements in the list returned are the affyIDs.
\code{which} can be "pm", "mm", or "both". If "both" then
perfect match locations are given followed by mismatch locations. 
\item[intensity<-] \code{signature(object = "AffyBatch")}: a
replacement method for the \code{exprs} slot, i.e. the intensities. 
\item[intensity] \code{signature(object = "AffyBatch")}: extract the
\code{exprs} slot, i.e. the intensities. 
\item[length] \code{signature(x = "AffyBatch")}: returns the number
of samples. 
\item[pmindex] \code{signature(object = "AffyBatch")}: return the
location of perfect matches in the intensity matrix.
\item[mmindex] \code{signature(object = "AffyBatch")}: return the
location of the mismatch intensities. 
\item[ncol] \code{signature(x = "AffyBatch")}: An accessor function
for \code{ncol}.
\item[nrow] \code{signature(x = "AffyBatch")}: an accessor function
for \code{nrow}.
\item[normalize] \code{signature(object = "AffyBatch")}: a method to
\code{\Link{normalize}}. The method accepts an argument
\code{method}. The default methods is specified in package options
(see the main vignette).

\item[normalize.methods] \code{signature(object = "AffyBatch")}:
returns the normalization methods defined for this class. See \code{\Link{normalize}}.
\item[probeNames] \code{signature(object = "AffyBatch")}: returns
the probe set associated with each row of the intensity matrix. 
\item[probeset] \code{signature(object = "AffyBatch",genenames=NULL,
        locations=NULL)}: Extracts \code{\Link{ProbeSet}} objects related to
the probe sets given in genenames. If an alternative set of
locations defining pms and mms a list with those locations should
be passed via the \code{locations} argument.
\item[bg.correct] \code{signature(object = "AffyBatch",
        method="character")} applies background correction methods
defined by method.
}\end{Section}
\begin{Note}\relax
This class is better described in the vignette.
\end{Note}
\begin{SeeAlso}\relax
related methods \code{\Link{merge.AffyBatch}},
\code{\Link{split.AffyBatch}} and \code{\Link{pairs.AffyBatch}}, and related classes \code{\Link{Cel}},
\code{\Link{Cdf}} and 
\code{\Link{exprSet-class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## load example
data(affybatch.example)

## nice print
print(affybatch.example)

pm(affybatch.example)[1:5,]
mm(affybatch.example)[1:5,]

## get indexes for the PM probes for the affyID "A28102_at" 
mypmindex <- pmindex(affybatch.example,"A28102_at")
## same operation using the primitive
mypmindex <- indexProbes(affybatch.example, which="pm", genenames="A28102_at")[[1]]
## get the probe intensities from the index
intensity(affybatch.example)[mypmindex, ]

## load bigger example (try 'help(Dilution)' )
data(affybatch.example)
description(affybatch.example) ##we can also use the methods of exprSet
sampleNames(affybatch.example)
abstract(affybatch.example)
\end{ExampleCode}
\end{Examples}

