normalizeAffyBatchConstantPara {affyPara}R Documentation

Parallelized scaling normalization

Description

Parallelized scaling normalization of arrays.

Usage

normalizeAffyBatchConstantPara(cluster,
      object,
      refindex = 1, FUN = mean, na.rm = TRUE,
      phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
      verbose = FALSE)  
       
normalizeConstantParaSF1(refindexname)
normalizeConstantParaSF2(refconstant, refindexname, FUN = mean, na.rm = TRUE)

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.
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.
verbose A logical value. If TRUE it writes out some messages.
refindexname The name of the array used as reference.
refconstant The constant calculated by FUN from the reference array. This value will be used for scaling.

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.

normalizeConstantParaSF1 and normalizeConstantParaSF2 are internal function which will be executed at all slaves.

normalizeConstantParaSF1
Calculates and returns intensities from the refindex array.
normalizeConstantParaSF2
Normalizes the arrays at all slaves.

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)

data(affybatch.example)

c1 <- makeCluster(3)

AffyBatch <- normalizeAffyBatchConstantPara(c1, affybatch.example, verbose=TRUE)

stopCluster(c1)
## End(Not run)

[Package affyPara version 1.0.0 Index]