normalizeAffyBatchQuantilesPara: Parallelized quantile normalization

In affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Description

Parallelized normalization of arrays based upon quantiles.

Usage

normalizeAffyBatchQuantilesPara(object,
    phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
    type = c("separate", "pmonly", "mmonly", "together"), 
    cluster, verbose = getOption("verbose"))

normalizeQuantilesPara(cluster, type, object.length, verbose = getOption("verbose"))

Arguments

object	An object of class AffyBatch OR a character vector with the names of CEL files OR a (partitioned) list of character vectors with CEL file names.
phenoData	An AnnotatedDataFrame object.
cdfname	Used to specify the name of an alternative cdf package. If set to NULL, the usual cdf package based on Affymetrix' mappings will be used.
type	A string specifying how the normalization should be applied.
cluster	A cluster object obtained from the function makeCluster in the SNOW package. For default .affyParaInternalEnv$cl will be used.
verbose	A logical value. If TRUE it writes out some messages. default: getOption("verbose")
object.length	Number of samples, which should be normalized.

Details

Parallelized normalization of arrays based upon quantiles. This method is based upon the concept of a quantile-quantile plot extended to n dimensions. No special allowances are made for outliers.

For the serial function and more details see the function normalize.AffyBatch.quantiles.

For using this function a computer cluster using the SNOW package has to be started. Starting the cluster with the command makeCluster generates an cluster object in the affyPara environment (.affyParaInternalEnv) and no cluster object in the global environment. The cluster object in the affyPara environment will be used as default cluster object, therefore no more cluster object handling is required. The makeXXXcluster functions from the package SNOW can be used to create an cluster object in the global environment and to use it for the preprocessing functions.

normalizeQuantilesPara is a internal function which will be executed at all slaves.

normalizeQuantilesPara

Function for quantile normalization.

Value

An AffyBatch of normalized objects.

Author(s)

Markus Schmidberger [e-mail], Ulrich Mansmann [e-mail]

Examples

## Not run: 
library(affyPara)
if (require(affydata)) {
  data(Dilution)

  makeCluster(3)

  AffyBatch <- normalizeAffyBatchQuantilesPara(Dilution, verbose=TRUE)

  stopCluster()
}

## End(Not run)

affyPara documentation built on Nov. 8, 2020, 11:08 p.m.