ScaleNormalization: The ScaleNormalization class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

ScaleNormalization

R Documentation

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