\name{combineData}
\alias{combineData}
\title{Combine two ExpressionSet objects}
\usage{
  combineData(object01, object02, obj01Var = "intensity",
    obj02Var = "intensity", runtype = "ff",
    saveFile = "combData")
}
\arguments{
  \item{object01}{An instance of
  \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}}
  either with SNP or non-polymorphic data}

  \item{object02}{An instance of
  \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}}
  either with SNP or non-polymorphic data}

  \item{obj01Var}{States the variable which should be
  combined from the assayData slot. Default is intensity.}

  \item{obj02Var}{States the variable which should be
  combined from the assayData slot. Default is intensity.}

  \item{runtype}{Mode how the results are saved. Possible
  values are ff or bm. If ff is chosen the data will not be
  saved automatically. With bm the results will be saved
  permanently.}

  \item{saveFile}{Name of the file to save.}
}
\value{
  An instance of
  \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}}.
}
\description{
  Suitable for SNP or non-polymorphic data which were
  already processed with single locus FARMS
}
\examples{
load(system.file("exampleData/normData.RData", package = "cn.farms"))
notes(experimentData(normData))$annotDir <-
        system.file("exampleData/annotation/pd.genomewidesnp.6/1.1.0",
                package = "cn.farms")
summaryMethod <- "Variational"
summaryParam <- list()
summaryParam$cyc <- c(10)
slData <- slSummarization(normData,
        summaryMethod = summaryMethod,
        summaryParam = summaryParam)
assayData(slData)$L_z[1:10, ]
combData <- combineData(slData, slData)
combData
}
\author{
  Djork-Arne Clevert \email{okko@clevert.de} and Andreas
  Mitterecker \email{mitterecker@bioinf.jku.at}
}