AbstractProbeSequenceNormalization: The AbstractProbeSequenceNormalization class

Description

Package: aroma.affymetrix Class AbstractProbeSequenceNormalization

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

Directly known subclasses: BaseCountNormalization, BasePositionNormalization, LinearModelProbeSequenceNormalization, MatNormalization

public abstract static class AbstractProbeSequenceNormalization extends ProbeLevelTransform3

This abstract class represents a normalization method that corrects for systematic effects in the probe intensities due to differences in probe sequences.

Usage

AbstractProbeSequenceNormalization(..., target=NULL)

Arguments

...

Arguments passed to the constructor of ProbeLevelTransform3.

target

A character string specifying type of "target" used. If "zero", all arrays are normalized to have no effects. If NULL, all arrays a normalized to have the same effect as the average array has.

Fields and Methods

Methods:

	`getTargetFile`
-
`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, objectSize, print, save, asThis

Requirements

This class requires that an AromaCellSequenceFile is available for the chip type.