normalizeNpData: Processes the non-polymorphic data
In mitterecker/cn.farms: cn.FARMS - factor analysis for copy number estimation

Description Usage Arguments Value Author(s) Examples

Normalization for non-polymorphic data for Affymetrix SNP5 and SNP6

1 2	normalizeNpData(filenames, cores = 1, annotDir = NULL, runtype = "ff", saveFile = "npData", method = c("baseline", "quantiles", "none"))

`filenames`	the absolute path of the CEL files as a list
`cores`	number of cores for used for parallelization
`annotDir`	Optional annotation directory.
`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.
`saveFile`	Name of the file to save.
`method`	The method for the normalization.

An instance of ExpressionSet containing the non-polymorphic data of the microarray.

Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at

## Not run: 
library("hapmapsnp6")
celDir <- system.file("celFiles", package = "hapmapsnp6")
filenames <- dir(path = celDir, full.names = TRUE)
createAnnotation(filenames = filenames)
npData <- normalizeNpData(filenames)

## End(Not run)