normalizeAffyBatchQuantilesPara {affyPara}R Documentation

Parallelized quantile normalization

Description

Parallelized normalization of arrays based upon quantiles.

Usage

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

normalizeQuantilesPara(cluster, type, object.length, verbose=FALSE)
normalizeQuantilesParaSF1(type)
normalizeQuantilesParaSF2(row_mean)

Arguments

cluster A cluster object obtained from the function makeCluster in the SNOW package.
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.
verbose A logical value. If TRUE it writes out some messages.
object.length Number of samples, which should be normalized.
row_mean Row mean used for normalization.

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.

normalizeQuantilesPara, normalizeQuantilesParaSF1 and normalizeQuantilesParaSF2 are internal function which will be executed at all slaves.

normalizeQuantilesPara
Function for quantil normalization.
normalizeQuantilesParaSF1
Slavefuntion to calculate row means.
normalizeQuantilesParaSF2
Slavefunction to do normalization.

Value

An AffyBatch of normalized objects.

Author(s)

Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann mansmann@ibe.med.uni-muenchen.de

Examples

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

  c1 <- makeCluster(3)

  AffyBatch <- normalizeAffyBatchQuantilesPara(c1, Dilution, verbose=TRUE)

  stopCluster(c1)
}
## End(Not run)

[Package affyPara version 1.2.1 Index]