normalizeAffyBatchLoessPara {affyPara}R Documentation

Parallelized loess normalization

Description

Parallelized loess normalization of arrays.

Usage

normalizeAffyBatchLoessPara(cluster,
        object,
        phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
        type=c("separate","pmonly","mmonly","together"), 
        subset = NULL,
        epsilon = 10^-2, maxit = 1, log.it = TRUE, 
        span = 2/3, family.loess ="symmetric",
        verbose=FALSE) 

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.
subset a subset of the data to fit a loess to.
epsilon a tolerance value (supposed to be a small value - used as a stopping criterium).
maxit maximum number of iterations.
log.it logical. If TRUE it takes the log2 of mat
span parameter to be passed the function loess
family.loess parameter to be passed the function loess. "gaussian" or "symmetric" are acceptable values for this parameter.
verbose A logical value. If TRUE it writes out some messages.

Details

Parallelized loess normalization of arrays.

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

For using this function a computer cluster using the snow package has to be started. In the loess normalization the arrays will compared by pairs. Therefore at every node minimum two arrays have to be!

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 <- normalizeAffyBatchLoessPara(c1, Dilution, verbose=TRUE)

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

[Package affyPara version 1.2.1 Index]