ScaleNormalization: The ScaleNormalization class

Description

Package: aroma.affymetrix Class ScaleNormalization

Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--ScaleNormalization

Directly known subclasses:

public static class ScaleNormalization extends ProbeLevelTransform

This class represents a normalization function that transforms the probe-level signals towards the same scale.

Usage

ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL, typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)

Arguments

dataSet

AffymetrixCelSet to be normalized.

...

Arguments passed to the constructor of ProbeLevelTransform.

targetAvg

A numeric value.

subsetToUpdate

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

typesToUpdate

Types of probes to be updated.

subsetToAvg

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

typesToAvg

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

shift

Optional amount of shift if data before fitting/normalizing.

Fields and Methods

Methods:

	`process`
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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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis