BaseCountNormalization: The BaseCountNormalization class

Description

Package: aroma.affymetrix
Class BaseCountNormalization

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--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, getParameters, getTargetFile, indexOfMissingSequences, predictOne, process

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

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

Requirements

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

Author

Henrik Bengtsson