aroma.affymetrix (version 2.11.1)

QuantileNormalization: The QuantileNormalization class

Description

Package: aroma.affymetrix Class QuantileNormalization Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--QuantileNormalization Directly known subclasses: DChipQuantileNormalization public static class QuantileNormalization extends ProbeLevelTransform This class represents a normalization function that transforms the probe-level signals towards the same empirical distribution.

Usage

QuantileNormalization(..., subsetToUpdate=NULL, typesToUpdate=NULL,
  targetDistribution=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform.

subsetToUpdate

The probes to be updated. If NULL, all probes are updated.

typesToUpdate

Types of probes to be updated.

targetDistribution

A numeric vector. The empirical distribution to which all arrays should be normalized to.

subsetToAvg

The probes to calculate average empirical distribution over. If a single numeric in (0,1), then this fraction of all probes will be used. If NULL<

typesToAvg

Types of probes to be used when calculating the average empirical distribution. If "pm" and "mm" only perfect-match and mismatch probes are used, respectively. If "pmmm" both types are used.

Fields and Methods

Methods: rll{ process Normalizes the data set. }

Methods inherited from ProbeLevelTransform: getRootPath

Methods inherited from Transform: getOutputDataSet, getOutputFiles

Methods inherited from AromaTransform: as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags

Methods inherited from ParametersInterface: getParameterSets, getParameters, getParametersAsString

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

Examples

for (zzz in 0) {

# Setup verbose output
verbose <- Arguments$getVerbose(-2)
timestampOn(verbose)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Define an example dataset
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Find any dataset
path <- NULL
if (is.null(path))
  break

ds <- AffymetrixCelSet$fromFiles(path)
print(ds)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Normalization
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
norm <- QuantileNormalization(ds, subsetToAvg=1/3)
dsQN <- process(norm, verbose=verbose)
print(dsQN)

} # for (zzz in 0)
rm(zzz)