\HeaderA{AffyBatch-class}{Class AffyBatch}{AffyBatch.Rdash.class}
\aliasA{\$.AffyBatch}{AffyBatch-class}{.Rdol..AffyBatch}
\aliasA{AffyBatch}{AffyBatch-class}{AffyBatch}
\aliasA{AffyBatch,ANY}{AffyBatch-class}{AffyBatch,ANY}
\aliasA{bg.correct,AffyBatch,character-method}{AffyBatch-class}{bg.correct,AffyBatch,character.Rdash.method}
\aliasA{boxplot,AffyBatch-method}{AffyBatch-class}{boxplot,AffyBatch.Rdash.method}
\aliasA{cdfName}{AffyBatch-class}{cdfName}
\aliasA{cdfName,AffyBatch-method}{AffyBatch-class}{cdfName,AffyBatch.Rdash.method}
\methaliasA{cdfName,AffyBatch-method}{AffyBatch-class}{cdfName,AffyBatch.Rdash.method}
\aliasA{checkValidFilenames}{AffyBatch-class}{checkValidFilenames}
\aliasA{col,AffyBatch-method}{AffyBatch-class}{col,AffyBatch.Rdash.method}
\aliasA{computeExprSet,AffyBatch,character,character-method}{AffyBatch-class}{computeExprSet,AffyBatch,character,character.Rdash.method}
\aliasA{dim,AffyBatch-method}{AffyBatch-class}{dim,AffyBatch.Rdash.method}
\aliasA{exprs,AffyBatch-method}{AffyBatch-class}{exprs,AffyBatch.Rdash.method}
\aliasA{exprs<-,AffyBatch,ANY-method}{AffyBatch-class}{exprs<.Rdash.,AffyBatch,ANY.Rdash.method}
\aliasA{featureNames,AffyBatch-method}{AffyBatch-class}{featureNames,AffyBatch.Rdash.method}
\aliasA{featureNames<-,AffyBatch-method}{AffyBatch-class}{featureNames<.Rdash.,AffyBatch.Rdash.method}
\aliasA{geneNames}{AffyBatch-class}{geneNames}
\aliasA{geneNames,AffyBatch-method}{AffyBatch-class}{geneNames,AffyBatch.Rdash.method}
\aliasA{geneNames<\Rdash}{AffyBatch-class}{geneNames<.Rdash.}
\aliasA{geneNames<-,AffyBatch,ANY-method}{AffyBatch-class}{geneNames<.Rdash.,AffyBatch,ANY.Rdash.method}
\aliasA{getCdfInfo}{AffyBatch-class}{getCdfInfo}
\aliasA{getCdfInfo,AffyBatch-method}{AffyBatch-class}{getCdfInfo,AffyBatch.Rdash.method}
\aliasA{hist,AffyBatch-method}{AffyBatch-class}{hist,AffyBatch.Rdash.method}
\aliasA{image}{AffyBatch-class}{image}
\aliasA{image,AffyBatch-method}{AffyBatch-class}{image,AffyBatch.Rdash.method}
\aliasA{indexProbes}{AffyBatch-class}{indexProbes}
\aliasA{indexProbes,AffyBatch,character-method}{AffyBatch-class}{indexProbes,AffyBatch,character.Rdash.method}
\aliasA{indexProbes,AffyBatch,missing-method}{AffyBatch-class}{indexProbes,AffyBatch,missing.Rdash.method}
\aliasA{indexProbes,AffyBatch-method}{AffyBatch-class}{indexProbes,AffyBatch.Rdash.method}
\aliasA{initialize,AffyBatch-method}{AffyBatch-class}{initialize,AffyBatch.Rdash.method}
\aliasA{intensity}{AffyBatch-class}{intensity}
\aliasA{intensity,AffyBatch-method}{AffyBatch-class}{intensity,AffyBatch.Rdash.method}
\aliasA{intensity<\Rdash}{AffyBatch-class}{intensity<.Rdash.}
\aliasA{intensity<-,AffyBatch-method}{AffyBatch-class}{intensity<.Rdash.,AffyBatch.Rdash.method}
\aliasA{length,AffyBatch-method}{AffyBatch-class}{length,AffyBatch.Rdash.method}
\aliasA{mm,AffyBatch-method}{AffyBatch-class}{mm,AffyBatch.Rdash.method}
\aliasA{mm<-,AffyBatch,ANY-method}{AffyBatch-class}{mm<.Rdash.,AffyBatch,ANY.Rdash.method}
\aliasA{mmindex}{AffyBatch-class}{mmindex}
\aliasA{mmindex,AffyBatch-method}{AffyBatch-class}{mmindex,AffyBatch.Rdash.method}
\aliasA{pm,AffyBatch-method}{AffyBatch-class}{pm,AffyBatch.Rdash.method}
\aliasA{pm<-,AffyBatch,ANY-method}{AffyBatch-class}{pm<.Rdash.,AffyBatch,ANY.Rdash.method}
\aliasA{pmindex}{AffyBatch-class}{pmindex}
\aliasA{pmindex,AffyBatch-method}{AffyBatch-class}{pmindex,AffyBatch.Rdash.method}
\aliasA{probeNames,AffyBatch-method}{AffyBatch-class}{probeNames,AffyBatch.Rdash.method}
\aliasA{probes}{AffyBatch-class}{probes}
\aliasA{probes,AffyBatch-method}{AffyBatch-class}{probes,AffyBatch.Rdash.method}
\aliasA{probeset}{AffyBatch-class}{probeset}
\aliasA{probeset,AffyBatch-method}{AffyBatch-class}{probeset,AffyBatch.Rdash.method}
\aliasA{row,AffyBatch-method}{AffyBatch-class}{row,AffyBatch.Rdash.method}
\aliasA{se.exprs,AffyBatch-method}{AffyBatch-class}{se.exprs,AffyBatch.Rdash.method}
\aliasA{se.exprs<-,AffyBatch-method}{AffyBatch-class}{se.exprs<.Rdash.,AffyBatch.Rdash.method}
\aliasA{show,AffyBatch-method}{AffyBatch-class}{show,AffyBatch.Rdash.method}
\aliasA{updateObject,AffyBatch-method}{AffyBatch-class}{updateObject,AffyBatch.Rdash.method}
\aliasA{[,AffyBatch-method}{AffyBatch-class}{[,AffyBatch.Rdash.method}
\aliasA{[<-,AffyBatch-method}{AffyBatch-class}{[<.Rdash.,AffyBatch.Rdash.method}
\aliasA{[[,AffyBatch-method}{AffyBatch-class}{[[,AffyBatch.Rdash.method}
\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. It extends \code{\LinkA{eSet}{eSet}}.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created using the function \code{\LinkA{read.affybatch}{read.affybatch}}
or the wrapper \code{\LinkA{ReadAffy}{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{integer} representing
the physical number of rows in the arrays.
\item[\code{ncol}:] Object of class \code{integer} representing
the physical number of columns in the arrays.
\item[\code{assayData}:] Object of class \code{AssayData}
containing the raw data, which will be at minimum a matrix of
intensity values. This slot can also hold a matrix of standard
errors if the 'sd' argument is set to \code{TRUE} in the call to \code{ReadAffy}. 
\item[\code{phenoData}:] Object of class \code{AnnotatedDataFrame}
containing phenotypic data for the samples.
\item[\code{annotation}] A character string identifying the
annotation that may be used for the \code{ExpressionSet}
instance.
\item[\code{featureData}] Object of class \code{AnnotatedDataFrame}
containing feature-level (e.g., probeset-level) information.
\item[\code{experimentData}:] Object of class "MIAME" containing
experiment-level information. 
\item[\code{notes}:] Object of class "character" Vector of
explanatory text 
}
\end{Section}
\begin{Section}{Extends}
Class \code{"eSet"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[cdfName] \code{signature(object = "AffyBatch")}: Obtains the
cdfName slot.
\item[pm\textless{}-] \code{signature(object = "AffyBatch")}: replaces the
perfect match intensities 
\item[pm] \code{signature(object = "AffyBatch")}: extracts the pm intensities. 
\item[mm\textless{}-] \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[exprs] \code{signature(object = "AffyBatch")}: extracts the
expression matrix.
\item[exprs\textless{}-] \code{signature(object = "AffyBatch", value = "matrix")}: replaces the
expression matrix.
\item[se.exprs] \code{signature(object = "AffyBatch")}: extracts the
matrix of standard errors of expression values, if available.
\item[se.exprs\textless{}-] \code{signature(object = "AffyBatch", value = "matrix")}: replaces the
matrix of standard errors of expression values.
\item[[\textless{}-] \code{signature(x = "AffyBatch")}: replaces subsets. 
\item[[] \code{signature(x = "AffyBatch")}: subsets by array.
\item[boxplot] \code{signature(x = "AffyBatch")}:  creates a
\code{\LinkA{boxplot}{boxplot}s of log base 2 intensities (pm, mm or
        both). Defaults to both.}
\item[hist] \code{signature(x = "AffyBatch")}:  creates a
plot showing all the histograms of the pm,mm or both data. See
\code{\LinkA{plotDensity}{plotDensity}}
\item[computeExprSet] \code{signature(x = "AffyBatch",
        summary.method = "character")}: For each probe set computes an
expression value using \code{summary.method}. 
\item[featureNames] \code{signature(object = "AffyBatch")}: return the
probe set names also referred to as the Affymetrix IDs. Notice
that one can not assign \code{featureNames}. You must do this by changing
the cdfenvs.
\item[geneNames] \code{signature(object="AffyBatch'")}: deprecated,
use \code{featureNames}
\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.

\code{signature(object = "AffyBatch", which = "missing")} (i.e.,
calling \code{indexProbes} without a "which" argument) is the
same as setting "which" to "pm".
 
\item[intensity\textless{}-] \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[dim] \code{signature(x = "AffyBatch")}: Row and column dimensions.
\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{\LinkA{normalize}{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{\LinkA{normalize}{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{\LinkA{ProbeSet}{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.
\item[updateObject] \code{signature(object = "AffyBatch", ...,
        verbose=FALSE)}: update, if necessary, an object of class
AffyBatch to its current class definition. \code{verbose=TRUE}
provides details about the conversion process.
}
\end{Section}
\begin{Note}\relax
This class is better described in the vignette.
\end{Note}
\begin{SeeAlso}\relax
related methods \code{\LinkA{merge.AffyBatch}{merge.AffyBatch}},
\code{\LinkA{pairs.AffyBatch}{pairs.AffyBatch}}, and
\code{\LinkA{eSet}{eSet}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if (require(affydata)) {
  ## load example
  data(Dilution)

  ## nice print
  print(Dilution)

  pm(Dilution)[1:5,]
  mm(Dilution)[1:5,]

  ## get indexes for the PM probes for the affyID "1900_at" 
  mypmindex <- pmindex(Dilution,"1900_at")
  ## same operation using the primitive
  mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
  ## get the probe intensities from the index
  intensity(Dilution)[mypmindex, ]

  description(Dilution) ##we can also use the methods of eSet
  sampleNames(Dilution)
  abstract(Dilution)
}
\end{ExampleCode}
\end{Examples}

