BaseCountNormalization {aroma.affymetrix}R Documentation

The BaseCountNormalization class

Description

Package: aroma.affymetrix
Class BaseCountNormalization

Object
~~|
~~+--AromaTransform
~~~~~~~|
~~~~~~~+--Transform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform3
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AbstractProbeSequenceNormalization
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--BaseCountNormalization

Directly known subclasses:

public static class BaseCountNormalization
extends AbstractProbeSequenceNormalization

This class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in the number of A, C, G, and T:s in the probe sequences.

Usage

BaseCountNormalization(..., model=c("robustSmoothSpline", "lm"), bootstrap=FALSE)

Arguments

... Arguments passed to the constructor of AbstractProbeSequenceNormalization.
model A character string specifying the model used to fit the base-count effects.
bootstrap If TRUE, the model fitting is done by bootstrap in order to save memory.

Fields and Methods

Methods:
No methods defined.

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getTargetFile, indexOfMissingSequences, predictOne, process

Methods inherited from ProbeLevelTransform3:
clearCache, getCellsTo, getCellsToFit, getCellsToUpdate, getUnitsTo, getUnitsToFit, getUnitsToUpdate, writeSignals

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

Requirements

This class requires that an aroma probe sequence file is available for the chip type.

Author(s)

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


[Package aroma.affymetrix version 1.2.0 Index]