\name{normalizeNpData}
\alias{normalizeNpData}
\title{Processes the non-polymorphic data}
\usage{
  normalizeNpData(filenames, cores = 1, annotDir = NULL,
  runtype = "ff", saveFile = "npData", method =
  c("baseline", "quantiles"))
}
\arguments{
  \item{filenames}{the absolute path of the CEL files as a
  list}

  \item{cores}{number of cores for used for
  parallelization}

  \item{annotDir}{Optional annotation directory.}

  \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.}

  \item{method}{The method for the normalization.}
}
\value{
  An instance of
  \code{\link[Biobase:ExpressionSet-class]{ExpressionSet}}
  containing the non-polymorphic data of the microarray.
}
\description{
  Normalization for non-polymorphic data for Affymetrix
  SNP5 and SNP6
}
\examples{
\dontrun{
library("hapmapsnp6")
celDir <- system.file("celFiles", package="hapmapsnp6")
filenames <- dir(path=celDir, full.names=TRUE)
createAnnotation(filenames=filenames)
npData <- normalizeNpData(filenames)
}
}
\author{
  Djork-Arne Clevert \email{okko@clevert.de} and Andreas
  Mitterecker \email{mitterecker@bioinf.jku.at}
}