AbstractProbeSequenceNormalization
Acad
Achim
AdditiveCovariatesNormalization
AfAm
AffineCnPlm
AffinePlm
AffineSnpPlm
AffyBatch
AffyGenePDInfo
AffymetrixCdfFile
AffymetrixCelFile
AffymetrixCelSet
AffymetrixCelSetReporter
AffymetrixCelSetTuple
AffymetrixCnChpFile
AffymetrixCnChpSet
AffymetrixFile
AffymetrixFileSet
AffymetrixFileSetReporter
AffymetrixPgfFile
AffymetrixProbeTabFile
AlleleSummation
AllelicCrosstalkCalibration
AppVeyor
AromaChipTypeAnnotationFile
AromaMicroarrayDataFile
AromaMicroarrayDataSet
AromaMicroarrayDataSetList
AromaMicroarrayDataSetTuple
AromaPlatformInterface
AromaTabularBinaryFile
AromaTabularBinarySet
AromaTransform
AromaUnitSignalBinaryFile
AromaUnitSignalBinarySet
AromaUnitTabularBinaryFile
ArrayExplorer
AvgCnPlm
AvgPlm
AvgSnpPlm
BPMAP
BackgroundCorrection
BaseCountNormalization
BasePositionNormalization
Benchmarking
Bioinformatics
Bolstad
Bolstad's
CDF's
CEL
CFH
CHP
CMD
CN
CNAG
CNs
CRMA
CacheKeyInterface
Carvalho
ChIP
ChipDB
ChipDb
ChipEffectFile
ChipEffectGroupMerge
ChipEffectSet
ChipEffectSetTuple
ChipEffectTransform
ChromosomalModel
CnChipEffectFile
CnChipEffectSet
CnPlm
CnProbeAffinityFile
CnagCfhFile
CnagCfhSet
ColumnNamesInterface
Conboy
CopyNumberDataFile
CopyNumberDataSet
CrlmmModel
CrlmmParametersFile
CrlmmParametersSet
CustomSeq
DCP
DChip
DChipCdfBinFile
DChipDcpFile
DChipDcpSet
DChipGenomeInformation
DChipQuantileNormalization
DChipSnpInformation
DSC
EBImage
ExonChipEffectFile
ExonChipEffectSet
ExonProbeAffinityFile
ExonRmaPlm
ExpressionSet
FIRMA
FeatureSet
FileCacheKeyInterface
FirmaFile
FirmaModel
FirmaSet
FragmentEquivalentClassNormalization
FragmentLengthNormalization
Friedrich
FullNameInterface
GC
GCRMA
GcContentNormalization
GcRmaBackgroundCorrection
GeneChip
GenericDataFile
GenericDataFileSet
GenericDataFileSetList
GenericReporter
GenericTabularFile
GenericTabularFileSet
GenomeInformation
GenomeWideSNP
Gottardo
HB
HetLogAddCnPlm
HetLogAddPlm
HetLogAddSnpPlm
Hooiveld
Hornik
Hossjer
HuEx
Irizarry
Isoforms
IxK
JS
Jitter
Jx
JxK
Lapuk
Leisch
LimmaBackgroundCorrection
LinearModelProbeSequenceNormalization
Liu
MBEI
MMs
MatNormalization
MatSmoothing
MbeiCnPlm
MbeiPlm
MbeiSnpPlm
MultiArrayUnitModel
Multichip
NAR
NetAffx
NormExpBackgroundCorrection
Nx
OpticalBackgroundCorrection
PDInfo
PGF
PLM
PLMs
PMA
PMB
PNAS
ParameterCelFile
ParameterCelSet
ParametersInterface
ProbeAffinityFile
ProbeLevelModel
ProbeLevelTransform
Proc
QualityAssessmentFile
QualityAssessmentModel
QualityAssessmentSet
QuantileNormalization
RMA
Reproducibility
Rescaling
ReseqCrosstalkCalibration
ResidualFile
ResidualSet
RmaBackgroundCorrection
RmaCnPlm
RmaPlm
RmaSnpPlm
ScaleNormalization
SingleArrayUnitModel
SmoothMultiarrayModel
SmoothRmaModel
SnpChipEffectFile
SnpChipEffectGroupMerge
SnpChipEffectSet
SnpInformation
SnpPlm
SnpProbeAffinityFile
SpatialReporter
SpatialRowColumnNormalization
Subclasses
TABs
TabularTextFile
Thinkpad
TransformReport
UFC
UGC
UGP
UgpGenomeInformation
UnitAnnotationDataFile
UnitModel
UnitNamesFile
UnitTypeScaleNormalization
UnitTypesFile
Veitch
WEHI
WeightsFile
WeightsSet
Wirapati
Wuest
Xba
Zeileis
addIncludes
addIndexFile
affine
affy
affymetrix
al
allelic
allocateFromCdf
allocateFromUnitAnnotationDataFile
allocateFromUnitNamesFile
anyDuplicated
anyNA
appendColumnNamesTranslator
appendColumnNamesTranslatorByNULL
appendColumnNamesTranslatorBycharacter
appendColumnNamesTranslatorByfunction
appendColumnNamesTranslatorBylist
appendFiles
appendFullNameTranslator
appendFullNameTranslatorByNULL
appendFullNameTranslatorByTabularTextFile
appendFullNameTranslatorByTabularTextFileSet
appendFullNameTranslatorBycharacter
appendFullNameTranslatorBydata
appendFullNameTranslatorByfunction
appendFullNameTranslatorBylist
appendFullNamesTranslator
appendFullNamesTranslatorByNULL
appendFullNamesTranslatorByTabularTextFile
appendFullNamesTranslatorByTabularTextFileSet
appendFullNamesTranslatorBydata
appendFullNamesTranslatorByfunction
appendFullNamesTranslatorBylist
asThis
assertDuplicates
attachLocally
averageQuantile
basepairs
boxplotStats
byChipType
byName
byPath
calculateAverageColumnAcrossFiles
calculateBaseline
calculateFieldBoxplotStats
calculateNuseBoxplotStats
calculateResidualSet
calculateRleBoxplotStats
calculateWeights
cdf
chiptype
chromsome
chromsosomes
clearCache
clearColumnNamesTranslator
clearFullNameTranslator
clearFullNamesTranslator
clearListOfColumnNamesTranslators
clearListOfFullNameTranslators
clearLookupCache
colApply
colMeans
colStats
colSums
combineAlleles
compareChecksum
convertToUnique
copyTo
createFrom
createOutputTuple
crosstalk
dChip
dTheta
dcp
doCBS
doCRMAv
doFIRMA
doGCRMA
doRMA
dsApplyInPairs
eps
et
exportTotalAndFracB
extractAffyBatch
extractAlleleSet
extractCNT
extractChromosomalDataFrame
extractDataFrame
extractExpressionSet
extractFeatureSet
extractMatrix
extractRawGenomicSignals
extractSnpCnvQSet
extractSnpFeatureSet
extractSnpQSet
extractTheta
extractTotalAndFracB
extractTotalAndFreqB
findByChipType
findByName
findDuplicated
findFilesTodo
findTargetDistributionFile
findUnitsTodo
fitOne
fitOneChromosome
fromCdf
fromDataSet
fromFile
getAM
getAlias
getAm
getAromaCellSequenceFile
getAromaFullNameTranslatorSet
getAromaGenomeTextFile
getAromaPlatform
getAromaUflFile
getAromaUgpFile
getArraysOfInput
getAsFullCelFile
getAsFullCelSet
getAsteriskTags
getAttribute
getAttributeXY
getAttributes
getAverage
getAverageAsinh
getAverageFile
getAverageLog
getBandwidth
getBaseline
getBytesPerColumn
getCacheKey
getCalculateResidualsFunction
getCdf
getCellIndices
getCellMapForMainCdf
getCellsTo
getCellsToFit
getCellsToUpdate
getChecksum
getChecksumFile
getChecksumFileSet
getChecksumObjects
getChipEffectSet
getChipType
getChipTypes
getChromosomeStats
getChromosomes
getColClasses
getColumnNames
getColumnNamesTranslator
getCombineAlleles
getCommentChar
getCovariates
getCreatedOn
getData
getDataSet
getDefaultColumnClassPatterns
getDefaultColumnClasses
getDefaultColumnNames
getDefaultExtension
getDefaultFullName
getDesignMatrix
getEnvironment
getExpandedCellMap
getExpectedOutputFiles
getExpectedOutputFullnames
getExtension
getExtensionPattern
getFieldModifier
getFieldModifiers
getFields
getFile
getFileClass
getFileFormat
getFileList
getFileListClass
getFileSet
getFileSize
getFileType
getFilename
getFilenameExtension
getFiles
getFitSingleCellUnitFunction
getFitUnitGroupFunction
getFragmentLengths
getFragmentStarts
getFragmentStops
getFullName
getFullNameTranslator
getFullNameTranslatorSet
getFullNames
getGenome
getGenomeData
getGenomeFile
getHeader
getImage
getIncludePath
getInputDataSet
getInputName
getInputTags
getInstantiationTime
getIntensities
getLastAccessedOn
getLastModifiedOn
getListOfAromaUgpFiles
getListOfColumnNamesTranslators
getListOfFullNameTranslators
getListOfGenomeInformations
getListOfPriors
getMainPath
getMergeFunction
getMergeStrands
getName
getNameOfInput
getNames
getNormalEquations
getNumberOfFilesAveraged
getOneFile
getOutputDataSet
getOutputExtension
getOutputFiles
getOutputTuple
getParameterSets
getParameters
getParametersAsString
getParentName
getParentPath
getPath
getPathname
getPathnames
getPcuTheta
getPlatform
getPloidy
getPositionChipTypeUnit
getPositions
getProbeAffinityFile
getReadArguments
getReportPath
getReportPathPattern
getReportSet
getResidualSet
getRlmFitFunctions
getRootName
getRootPath
getSampleLayerPrefix
getSet
getSetTuple
getSets
getSignalTransform
getStaticInstance
getSubdirs
getSubname
getTags
getTagsOfInput
getTargetFile
getTemplatePath
getTimestamps
getUnitAnnotationDataFile
getUnitGroupCellArrayMap
getUnitGroupCellMap
getUnitGroupCellMatrixMap
getUnitIndices
getUnitIntensities
getUnitNames
getUnitNamesFile
getUnitTypes
getUnitTypesFile
getUnitsOnChromosome
getUnitsOnChromosomes
getUnitsTo
getUnitsToFit
getUnitsToUpdate
getVersion
getWeightsSet
getXAM
groupdirection
gunzip
gzip
hasAlleleBFractions
hasAttributeXY
hasBeenModified
hasColumnHeader
hasField
hasFile
hasStrandiness
hasTag
hasTags
hashCode
hg
importFrom
indexOf
indexOfMissingSequences
instanciated
isAverageFile
isCompatibleWith
isCompatibleWithCdf
isDone
isDuplicated
isFile
isGzipped
isOutlier
iter
jitter
june
justRMA
justSNPRMA
lexicographically
linkTo
macOS
mergeGroups
mergeStrands
monocell
multimapping
na
nbr
nbrOfArrays
nbrOfCells
nbrOfChipTypes
nbrOfColumns
nbrOfEnzymes
nbrOfFiles
nbrOfLines
nbrOfRows
nbrOfSets
nbrOfUnits
ngroups
normalizeQuantile
nucleotides
objectSize
oo
pbase
pdInfo
ploidy
plotBoxplot
plotDensity
plotImage
plotMvsA
plotMvsX
preceeding
predictOne
probeWindow
probepairs
probeset
probesets
readChecksum
readColumnNames
readColumns
readDataFrame
readFooter
readHeader
readLines
readRawFooter
readRawHeader
readUnits
reconstructor
renameTo
renameToUpperCaseExt
rescale
rescaled
rescaling
resequence
resequencing
resetFullName
resetFullNames
sd
setAlias
setArrays
setAttribute
setAttributeXY
setAttributes
setAttributesBy
setAttributesBySampleAnnotationFile
setAttributesBySampleAnnotationSet
setAttributesByTags
setBandwidth
setCdf
setChromosomes
setColumnNames
setColumnNamesTranslator
setCombineAlleles
setCommentChar
setExtensionPattern
setFullName
setFullNameTranslator
setFullNamesTranslator
setGenome
setListOfColumnNamesTranslators
setListOfFullNameTranslators
setListOfPriors
setMergeFunction
setMergeStrands
setName
setReportPathPattern
setSubname
setTags
smoothScatterMvsA
snp
sortBy
splitByReportPathPattern
stddevs
subclasses
subclassing
summarization
tbase
testAttributes
th
updateColumnNames
updateData
updateDataColumn
updateFullName
updateFullNames
updateSetupExplorerFile
updateUnits
validateChecksum
writeAsFullCelFile
writeCNT
writeChecksum
writeColumnsToFiles
writeDataFrame
writeFooter
writeImage
writeRawFooter
writeSgr
writeSignals
xK
xls
xrange
yrange
