aroma.affymetrix (version 2.2.0)

DChipQuantileNormalization: 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.

Fields and Methods

Methods: rll{ process Normalizes the data set. } Methods inherited from QuantileNormalization: clearCache, findTargetDistributionFile, 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, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

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.