DChipQuantileNormalization {aroma.affymetrix} | R Documentation |
The DChipQuantileNormalization class
Description
Package: aroma.affymetrix
Class DChipQuantileNormalization
Object
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~~+--
ParametersInterface
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AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
QuantileNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--
DChipQuantileNormalization
Directly known subclasses:
public static class DChipQuantileNormalization
extends QuantileNormalization
This class represents a special QuantileNormalization
using smooth-splines.
Usage
DChipQuantileNormalization(..., robust=FALSE)
Arguments
... |
Arguments passed to the constructor of
|
robust |
If |
Details
This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).
Fields and Methods
Methods:
process | - | |
Methods inherited from QuantileNormalization:
findTargetDistributionFile, getParameters, 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
Author(s)
Henrik Bengtsson
References
[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.