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ChipEffectSet {aroma.affymetrix}

The ChipEffectSet class
Package: 
aroma.affymetrix
Version: 
2.9.0

Description

Package: aroma.affymetrix
Class ChipEffectSet

Object
~~|
~~+--FullNameInterface
~~~~~~~|
~~~~~~~+--GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaMicroarrayDataSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParametersInterface
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectSet

Directly known subclasses:
CnChipEffectSet, ExonChipEffectSet, SnpChipEffectSet

public static class ChipEffectSet
extends ParameterCelSet

This class represents estimates of chip effects in the probe-level models.

Usage

ChipEffectSet(..., probeModel=c("pm"))

Arguments

...
Arguments passed to AffymetrixCelSet.
probeModel
The specific type of model, e.g. "pm".

Fields and Methods

Methods:

boxplotStats -
extractExpressionSet Extracts an in-memory ExpressionSet object.
extractMatrix -
extractTheta -
findUnitsTodo -
getAM Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file.
getAverageFile -
getCellIndices -
plotBoxplot -
readUnits -

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

Methods inherited from AffymetrixCelSet:
append, as, as.AffymetrixCelSet, as.character, averageQuantile, byName, byPath, clone, convertToUnique, doCRMAv1, doCRMAv2, doFIRMA, doGCRMA, doRMA, extractAffyBatch, extractFeatureSet, extractMatrix, extractSnpFeatureSet, findByName, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, byPath, getDefaultFullName

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getAromaUgpFile, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith

Methods inherited from AromaMicroarrayDataSet:
as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, nbrOfArrays, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate

Methods inherited from GenericDataFileSet:
append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, clearCache, clearFullNamesTranslator, clone, copyTo, equals, extract, findByName, getChecksum, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, hasFile, indexOf, nbrOfFiles, resetFullNames, seq, setFullNamesTranslator, sortBy, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, getParentName

Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName

Methods inherited from Object:
$, $<-, [[, [[<-, 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, asThis

See Also

An object of this class is typically obtained through the getChipEffectSet() method for the ProbeLevelModel class.

Author(s)

Henrik Bengtsson

Documentation reproduced from package aroma.affymetrix, version 2.9.0. License: LGPL (>= 2.1)