ProbeLevelTransform3: The ProbeLevelTransform3 class

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

The ProbeLevelTransform3 class

Description

Package: aroma.affymetrix
Class ProbeLevelTransform3

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3

Directly known subclasses:
AbstractProbeSequenceNormalization, BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization, ScaleNormalization3, UnitTypeScaleNormalization

public abstract static class ProbeLevelTransform3
extends ProbeLevelTransform

This abstract class is specialized from ProbeLevelTransform and provides methods to identify subsets and types of probes that are used for fitting and/or updating the signals.

Usage

ProbeLevelTransform3(dataSet=NULL, ..., unitsToFit="-XY", typesToFit=typesToUpdate,
  unitsToUpdate=NULL, typesToUpdate="pm", shift=0)

Arguments

dataSet	A AffymetrixCelSet.
...	Arguments passed to the constructor of ProbeLevelTransform.
unitsToFit	The units from which the normalization curve should be estimated. If NULL, all are considered.
typesToFit	Types of probes to be used when fitting the model.
unitsToUpdate	The units to be updated. If NULL, all are considered.
typesToUpdate	Types of probes to be updated.
shift	An optional amount to shift data before fitting and updating.

Fields and Methods

Methods:
No methods defined.

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.