DChipQuantileNormalization {aroma.affymetrix}R Documentation

The DChipQuantileNormalization class

Description

Package: aroma.affymetrix
Class DChipQuantileNormalization

Object
~~|
~~+--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.

Details

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

Fields and Methods

Methods:
process Normalizes the data set.

Methods inherited from QuantileNormalization:
clearCache, process

Methods inherited from Transform:
getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles

Methods inherited from AromaTransform:
getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags

Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

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.


[Package aroma.affymetrix version 1.2.0 Index]