AbstractProbeSequenceNormalization
                        The AbstractProbeSequenceNormalization class
AdditiveCovariatesNormalization
                        The AdditiveCovariatesNormalization class
AffineCnPlm             The AffineCnPlm class
AffinePlm               The AffinePlm class
AffineSnpPlm            The AffineSnpPlm class
AffymetrixCdfFile       The AffymetrixCdfFile class
AffymetrixCelFile       The AffymetrixCelFile class
AffymetrixCelSet        The AffymetrixCelSet class
AffymetrixCelSetReporter
                        The AffymetrixCelSetReporter class
AffymetrixCelSetTuple   The AffymetrixCelSetTuple class
AffymetrixCnChpSet      The AffymetrixCnChpSet class
AffymetrixFile          The abstract AffymetrixFile class
AffymetrixFileSet       The AffymetrixFileSet class
AffymetrixFileSetReporter
                        The AffymetrixFileSetReporter class
AffymetrixPgfFile       The AffymetrixPgfFile class
AlleleSummation         The AlleleSummation class
AllelicCrosstalkCalibration
                        The AllelicCrosstalkCalibration class
AromaChipTypeAnnotationFile
                        The AromaChipTypeAnnotationFile class
ArrayExplorer           The ArrayExplorer class
AvgCnPlm                The AvgCnPlm class
AvgPlm                  The AvgPlm class
AvgSnpPlm               The AvgSnpPlm class
BackgroundCorrection    The BackgroundCorrection class
BaseCountNormalization
                        The BaseCountNormalization class
BasePositionNormalization
                        The BasePositionNormalization class
ChipEffectFile          The ChipEffectFile class
ChipEffectSet           The ChipEffectSet class
ChipEffectTransform     The ChipEffectTransform class
CnChipEffectFile        The CnChipEffectFile class
CnChipEffectSet         The CnChipEffectSet class
CnPlm                   The CnPlm class
CnProbeAffinityFile     The CnProbeAffinityFile class
CnagCfhFile             The CnagCfhFile class
CnagCfhSet              The CnagCfhSet class
CrlmmParametersFile     The CrlmmParametersFile class
CrlmmParametersSet      The CrlmmParametersSet class
DChipCdfBinFile         The DChipCdfBinFile class
DChipDcpFile            The DChipDcpFile class
DChipDcpSet             The DChipDcpSet class
DChipGenomeInformation
                        The DChipGenomeInformation class
DChipQuantileNormalization
                        The DChipQuantileNormalization class
DChipSnpInformation     The DChipSnpInformation class
ExonChipEffectFile      The ExonChipEffectFile class
ExonChipEffectSet       The ExonChipEffectSet class
ExonProbeAffinityFile   The ExonProbeAffinityFile class
ExonRmaPlm              The ExonRmaPlm class
FirmaFile               The FirmaFile class
FirmaModel              The FirmaModel class
FirmaSet                The FirmaSet class
FragmentEquivalentClassNormalization
                        The FragmentEquivalentClassNormalization class
FragmentLengthNormalization
                        The FragmentLengthNormalization class
GcContentNormalization
                        The GcContentNormalization class
GcContentNormalization2
                        The GcContentNormalization2 class
GcRmaBackgroundCorrection
                        The GcRmaBackgroundCorrection class
GenericReporter         The GenericReporter class
GenomeInformation       The GenomeInformation class
HetLogAddCnPlm          The HetLogAddCnPlm class
HetLogAddPlm            The HetLogAddPlm class
HetLogAddSnpPlm         The HetLogAddSnpPlm class
LimmaBackgroundCorrection
                        The LimmaBackgroundCorrection class
LinearModelProbeSequenceNormalization
                        The LinearModelProbeSequenceNormalization class
MatNormalization        The MatNormalization class
MatSmoothing            The MatSmoothing class
MbeiCnPlm               The MbeiCnPlm class
MbeiPlm                 The MbeiPlm class
MbeiSnpPlm              The MbeiSnpPlm class
Model                   The Model class
MultiArrayUnitModel     The MultiArrayUnitModel class
NormExpBackgroundCorrection
                        The NormExpBackgroundCorrection class
OpticalBackgroundCorrection
                        The OpticalBackgroundCorrection class
ParameterCelFile        The ParameterCelFile class
ParameterCelSet         The ParameterCelSet class
ProbeAffinityFile       The ProbeAffinityFile class
ProbeLevelModel         The ProbeLevelModel class
ProbeLevelTransform     The ProbeLevelTransform class
ProbeLevelTransform3    The ProbeLevelTransform3 class
QualityAssessmentFile   The QualityAssessmentFile class
QualityAssessmentModel
                        The QualityAssessmentModel class
QualityAssessmentSet    The QualityAssessmentSet class
QuantileNormalization   The QuantileNormalization class
ReseqCrosstalkCalibration
                        The ReseqCrosstalkCalibration class
ResidualFile            The ResidualFile class
ResidualSet             The ResidualSet class
RmaBackgroundCorrection
                        The RmaBackgroundCorrection class
RmaCnPlm                The RmaCnPlm class
RmaPlm                  The RmaPlm class
RmaSnpPlm               The RmaSnpPlm class
ScaleNormalization      The ScaleNormalization class
ScaleNormalization3     The ScaleNormalization3 class
SingleArrayUnitModel    The SingleArrayUnitModel class
SmoothMultiarrayModel   The SmoothMultiarrayModel class
SmoothRmaModel          The SmoothRmaModel class
SnpChipEffectFile       The SnpChipEffectFile class
SnpChipEffectSet        The SnpChipEffectSet class
SnpInformation          The SnpInformation class
SnpPlm                  The SnpPlm interface class
SnpProbeAffinityFile    The SnpProbeAffinityFile class
SpatialReporter         The SpatialReporter class
TransformReport         The TransformReport class
UgpGenomeInformation    The UgpGenomeInformation class
UnitModel               The UnitModel class
UnitTypeScaleNormalization
                        The UnitTypeScaleNormalization class
WeightsFile             The WeightsFile class
WeightsSet              The WeightsSet class
aroma.affymetrix-package
                        Package aroma.affymetrix
doCRMAv1                Estimation and assessment of raw copy numbers
                        at the single locus level (CRMA v1)
doCRMAv2                A single-array preprocessing method for
                        estimating full-resolution raw copy numbers
                        from all Affymetrix genotyping arrays (CRMA v2)
doFIRMA                 Finding Isoforms using Robust Multichip
                        Analysis (FIRMA)
doGCRMA                 Robust Multichip Analysis (GCRMA)
doRMA                   Robust Multichip Analysis (RMA)
justRMA                 Robust Multichip Analysis (RMA) reproducing the
                        affy package
