AffymetrixCelSet: The AffymetrixCelSet class

Description

Package: aroma.affymetrix Class AffymetrixCelSet

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFileSet ~~~~~~~~~~~~| ~~~~~~~~~~~~+--AromaMicroarrayDataSet ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixFileSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet

Directly known subclasses: ChipEffectSet, CnChipEffectSet, ExonChipEffectSet, FirmaSet, ParameterCelSet, QualityAssessmentSet, ResidualSet, SnpChipEffectSet, WeightsSet

public static class AffymetrixCelSet extends AffymetrixFileSet

An AffymetrixCelSet object represents a set of Affymetrix CEL files with identical chip types.

Usage

AffymetrixCelSet(files=NULL, ...)

Arguments

files

A list of AffymetrixCelFile:s.

...

Not used.

Fields and Methods

Methods:

	`as`
-
`as.AffymetrixCelSet`	-
	`byName`
-
`doCRMAv1`	-
	`doCRMAv2`
-
`doFIRMA`	-
	`doGCRMA`
-
`doRMA`	-
	`extractAffyBatch`
-
`extractFeatureSet`	-
	`extractMatrix`
-
`getAverage`	-
	`getAverageAsinh`
-
`getAverageFile`	-
	`getAverageLog`
-
`getCdf`	-
	`getChipType`
-
`getData`	-
	`getIntensities`
-
`getPlatform`	-
	`getTimestamps`
-
`getUnitGroupCellMap`	-
	`getUnitIntensities`
-
`getUnitNamesFile`	-
	`getUnitTypesFile`
-
`justSNPRMA`	-
	`plotDensity`
-
`readUnits`	-
	`setCdf`
-
`writeSgr`	-

Methods inherited from AffymetrixFileSet: as, as.AffymetrixFileSet, byPath, getDefaultFullName Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith Methods inherited from AromaMicroarrayDataSet: as.AromaMicroarrayDataSetList, as.AromaMicroarrayDataSetTuple, getAromaFullNameTranslatorSet, getAverageFile, getChipType, getDefaultFullName, getPlatform, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate Methods inherited from GenericDataFileSet: [, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApply, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, 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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

Description

Usage

Arguments

Fields and Methods

See Also