MatNormalization: The MatNormalization class

Description

Package: aroma.affymetrix Class MatNormalization

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

Directly known subclasses:

public static class MatNormalization 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 and the match scores according to MAT [1].

Usage

MatNormalization(..., unitsToFit=NULL, model=c("lm"), nbrOfBins=200)

Arguments

...

Arguments passed to the constructor of AbstractProbeSequenceNormalization.

unitsToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

model

A character string specifying the model used to fit the base-count effects.

nbrOfBins

The number of bins to use for the variance smoothing step.

Fields and Methods

Methods:

	`process`
-

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, objectSize, print, save, asThis

Requirements

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

References

[1] Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip, PNAS, 2006.