normalizeCels {cn.farms} | R Documentation

## Wrapper for the normalization functions

### Description

This functions provides different normalization methods for microarray data. At the moment only SOR and quantile normalization are implemented.

### Usage

    normalizeCels(filenames, method = c("SOR", "quantiles", "none"), cores = 1,
      alleles = FALSE, runtype = "bm", annotDir = NULL,
      saveFile = "normData", ...)

### Arguments

`filenames` | The absolute path of the CEL files as a list.
`method` | The normalization method. Possible methods so far: SOR, quantiles
`cores` | Number of cores for used for parallelization.
`alleles` | States if information for allele A and B should be given back.
`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.
`annotDir` | An optional annotation directory.
`saveFile` | Name of the file to save.
`...` | Further parameters for the normalization method.

### Value

An ExpressionSet object with the normalized data.

### 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)
    normData <- normalizeCels(filenames, method = "SOR")

    ## End(Not run)

[Package cn.farms version 1.40.0 Index]