MatNormalization {aroma.affymetrix}R Documentation

The MatNormalization class

Description

Package: aroma.affymetrix
Class MatNormalization

Object
~~|
~~+--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"), numChunks=25, numBins=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.
numChunks The number of chunks to split the data into to fit the model
numBins The number of bins to use for the variance smoothing step

Fields and Methods

Methods:
process Normalizes the data set.

Methods inherited from AbstractProbeSequenceNormalization:
fitOne, getAromaCellSequenceFile, getTargetFile, indexOfMissingSequences, predictOne, process

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 aroma probe sequence file and aroma match scores file is available for the chip type.

Author(s)

Mark Robinson, WEHI.

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.


[Package aroma.affymetrix version 1.2.0 Index]