normalizeNpData {cn.farms} | R Documentation

## Processes the non-polymorphic data

### Description

Normalization for non-polymorphic data for Affymetrix SNP5 and SNP6

### Usage

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

### Arguments

`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.

### Value

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

### Author(s)

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

### Examples

    ## 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)

[Package cn.farms version 1.36.0 Index]