normalizeAffyBatchInvariantsetPara {affyPara}R Documentation

Parallelized Invariante Set normalization

Description

Parallelized normalization of arrays using an invariant set.

Usage

normalizeAffyBatchInvariantsetPara(cluster,
    object,
    prd.td = c(0.003, 0.007), baseline.type = c("mean", "median", "pseudo-mean", "pseudo-median"),
    type = c("separate", "pmonly", "mmonly", "together"),
    phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
    verbose = FALSE)
    
    normalizeInvariantsetParaSF1(FUN, type)
    normalizeInvariantsetParaSF2(refindexname, rows, prd.td, baseline.chip)

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.
prd.td A cutoff parameter for normalization.
baseline.type Specify how to determine the baseline array (mean, median).
type A string specifying how the normalization should be applied.
phenoData A 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.
FUN A function generating a value from the intensities on an array. Typically mean or median.
refindexname The name of the array used as reference.
rows Number of rows which have to be changed.
baseline.chip The values of the array used as reference.

Details

Parallelized normalization of arrays using an invariant set. The set of invariant intensities between data and ref is found through an iterative process (based on the respective ranks the intensities). This set of intensities is used to generate a normalization curve by smoothing.

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

For using this function a computer cluster using the snow package has to be started.

normalizeInvariantsetParaSF1 and normalizeInvariantsetParaSF2 are internal function which will be executed at all slaves.

normalizeInvariantsetParaSF1
Calculates and returns a value from the intensities of an array.
normalizeInvariantsetParaSF2
Normalizes the arrays at 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 <- normalizeAffyBatchInvariantsetPara(c1, affybatch.example, verbose=TRUE)

stopCluster(c1)
## End(Not run)

[Package affyPara version 1.0.0 Index]