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.
ScaleNormalization(dataSet=NULL, ..., targetAvg=4400, subsetToUpdate=NULL,
typesToUpdate=NULL, subsetToAvg="-XY", typesToAvg=typesToUpdate, shift=0)
AffymetrixCelSet to be normalized.
Arguments passed to the constructor of
ProbeLevelTransform.
A numeric value.
The probes to be updated.
If NULL, all probes are updated.
Types of probes to be updated.
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.
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.
Optional amount of shift if data before fitting/normalizing.
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
Henrik Bengtsson