vsnPara: Parallel fir of the vsn model

In affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Description

These parallel functions fit the vsn model to intensity data in an AffyBatch. They hav the same functionality than the vsn methods in the vsn package but are implemented in parallel (and only supports an AffyBatch as input data).

Usage

vsn2Para(object, cluster,
	phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
	reference, subsample,
	..., 
	verbose = getOption("verbose")) 

justvsnPara(object, cluster,
		...,
		verbose = getOption("verbose")) 
	
vsnrmaPara(object, cluster,
	pmcorrect.method="pmonly", pmcorrect.param=list(),
	summary.method="medianpolish", summary.param=list(),
	ids=NULL,
	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.
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.
subsample	Integer of length 1. If specified, the model parameters are estimated from a subsample of the data of size subsample only, yet the fitted transformation is then applied to all data. For large datasets, this can substantially reduce the CPU time and memory consumption at a negligible loss of precision.
reference	Optional, a vsn object from a previous fit. If this argument is specified, the data are normalized "towards" an existing set of reference arrays whose parameters are stored in the object reference. If this argument is not specified, then the data are normalized "among themselves".
...	Further arguments that get passed and are similar to vsn2.
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")
pmcorrect.method	The name of the PM adjustement method.
pmcorrect.param	A list of parameters for pmcorrect.method (if needed/wanted).
summary.method	The method used for the computation of expression values
summary.param	A list of parameters to be passed to the summary.method (if wanted).
ids	List of ids for summarization

Details

For the serial function and more details see the function vsn2.

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)

  AB1 <- justvsnPara(Dilution, verbose=verbose )

  stopCluster()
}

## End(Not run)

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