AbstractProbeSequenceNormalization {aroma.affymetrix}R Documentation

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 arrays a normalized to have the same effect as the average array has.

Fields and Methods

Methods:
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, $, $<-, [[, [[<-, 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 AromaCellSequenceFile is available for the chip type.

Author(s)

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


[Package aroma.affymetrix version 1.2.0 Index]