\name{computeExprSetPara}
\alias{computeExprSetPara}

\title{ Parallel generate a set of expression values }
\description{
Parallel generation of a set of expression values from the probe pair information. The set of expression is returned as an ExpressionSet object. 
}
\usage{
computeExprSetPara(object,
    ids = NULL,
    pmcorrect.method, summary.method,
    summary.param = list(), pmcorrect.param = list(),
    phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
    cluster, verbose = getOption("verbose"))

}
\arguments{
   \item{object}{ An object of class \link[affy:AffyBatch-class]{AffyBatch} 
   		OR a \code{character} vector with the names of CEL files 
   		OR a (partitioned) list of \code{character} vectors with CEL file names.}
 
  \item{pmcorrect.method}{ The name of the PM adjustement method. }
  \item{pmcorrect.param}{ A list of parameters for \code{pmcorrect.method} (if needed/wanted). }
  \item{summary.method}{ The method used for the computation of expression values }
  \item{summary.param}{ A list of parameters to be passed to the \code{summary.method} (if wanted). }
  \item{ids}{ List of \code{ids} for summarization. }

  \item{phenoData}{ An \link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame} object. }
  \item{cdfname}{ Used to specify the name of an alternative cdf package. 
  		If set to \code{NULL}, the usual cdf package based on Affymetrix' mappings will be used. }
  \item{cluster}{ A cluster object obtained from the function \link[snow:snow-startstop]{makeCluster} in the SNOW package. 
  		For default \code{.affyParaInternalEnv$cl}  will be used. }
  \item{verbose}{ A logical value. If \code{TRUE} it writes out some messages. }
}
\details{
Parallelized preprocessing function, which goes from raw probe intensities to expression values in one steps: summarization

For the serial function and more details see the function \code{computeExprSet}.

For using this function a computer cluster using the SNOW package has to be started. 
Starting the cluster with the command \code{makeCluster} generates an cluster object in the affyPara environment (.affyParaInternalEnv) and 
no cluster object in the global environment. The cluster object in the affyPara environment will be used as default cluster object, 
therefore no more cluster object handling is required.  
The \code{makeXXXcluster} functions from the package SNOW can be used to create an cluster object in the global environment and 
to use it for the preprocessing functions.
}

\value{
An object of class \link[Biobase:class.ExpressionSet]{ExpressionSet}.
}

\author{ Markus Schmidberger \email{schmidb@ibe.med.uni-muenchen.de}, Ulrich Mansmann \email{mansmann@ibe.med.uni-muenchen.de} }

\examples{
\dontrun{
library(affyPara)
if (require(affydata)) {
  data(Dilution)

  makeCluster(3)

  esset <- computeExprSetPara(Dilution,
    pmcorrect.method = "pmonly",
    summary.method = "avgdiff",
    verbose = TRUE)

  stopCluster()
}
}
}

\keyword{programming}
\keyword{manip}