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.
ProbeLevelTransform3(dataSet=NULL, ..., unitsToFit="-XY", typesToFit=typesToUpdate,
unitsToUpdate=NULL, typesToUpdate="pm", shift=0)
A AffymetrixCelSet.
Arguments passed to the constructor of
ProbeLevelTransform.
The units from which the normalization curve should
be estimated. If NULL, all are considered.
Types of probes to be used when fitting the model.
The units to be updated.
If NULL, all are considered.
Types of probes to be updated.
An optional amount to shift data before fitting and updating.
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
Henrik Bengtsson