AbstractProbeSequenceNormalization: The AbstractProbeSequenceNormalization class

Description

Package: aroma.affymetrix Class AbstractProbeSequenceNormalization Object ~~| ~~+--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 ar

Fields and Methods

Methods: rll{ getTargetFile - process Normalizes the data set. } 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, 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

Requirements

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