DChipQuantileNormalization: The DChipQuantileNormalization class

Description

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.

Usage

DChipQuantileNormalization(..., robust=FALSE)

Arguments

...

Arguments passed to the constructor of QuantileNormalization.

robust

If TRUE, the normalization function is estimated robustly, otherwise not.

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, objectSize, print, save, asThis

Details

This normalization method implements the two-pass algorithm described in Bengtsson et al. (2008).

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.