Package: aroma.affymetrix
Class DChipQuantileNormalization
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--QuantileNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--DChipQuantileNormalization
Directly known subclasses:
public static class DChipQuantileNormalization
extends QuantileNormalization
This class represents a special QuantileNormalization
using smooth-splines.
DChipQuantileNormalization(..., robust=FALSE)
Arguments passed to the constructor of
QuantileNormalization.
If TRUE, the normalization function is estimated
robustly, otherwise not.
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
Henrik Bengtsson
This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).
[1] H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008.