normalizeAffyBatchConstantPara: Parallelized scaling normalization

In affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Description

Parallelized scaling normalization of arrays.

Usage

normalizeAffyBatchConstantPara(object, cluster,
      refindex = 1, FUN = mean, na.rm = TRUE,
      phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
      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.
refindex	The index of the array used as reference.
FUN	A function generating a value from the intensities on an array. Typically mean or median.
na.rm	Paramater passed to the function FUN. A logical value indicating whether NA values should be stripped before the computation proceeds.
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.
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")

Details

Parallelized scaling normalization of arrays. This means that all the array are scaled so that they have the same mean value.

For the serial function and more details see the function normalize.constant.

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.

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 <- normalizeAffyBatchConstantPara(Dilution, verbose=TRUE)

  stopCluster()
}

## End(Not run)

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