ScaleNormalization: The ScaleNormalization class

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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	-

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, names, objectSize, print, save, asThis

Author(s)

Henrik Bengtsson

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.