Package: aroma.affymetrix
Class BasePositionNormalization
Object
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~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
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~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
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~~~~~~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3
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~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--LinearModelProbeSequenceNormalization
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--BasePositionNormalization
Directly known subclasses:
public abstract static class BasePositionNormalization
extends LinearModelProbeSequenceNormalization
This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in positioning of A, C, G, and T:s in the probe sequences.
BasePositionNormalization(..., model=c("smooth.spline"), df=5)
Arguments passed to the constructor of
LinearModelProbeSequenceNormalization.
A character string specifying the model used to fit
the base-count effects.
The degrees of freedom of the model.
Methods:
No methods defined.
Methods inherited from LinearModelProbeSequenceNormalization:
fitOne, getDesignMatrix, getNormalEquations, getSignalTransform, predictOne
Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process
Methods inherited from ProbeLevelTransform3:
getAsteriskTags, getCellsTo, getCellsToFit, getCellsToUpdate, getParameters, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals
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, Mark Robinson