The AffineCnPlm class
The AffinePlm class
The AffymetrixCelSetReporter class
AromaChipTypeAnnotationFile
The AromaChipTypeAnnotationFile class
The ArrayExplorer class
The AffymetrixCelSetTuple class
The AffymetrixCnChpSet class
The AvgSnpPlm class
The BackgroundCorrection class
The abstract AffymetrixFile class
AbstractProbeSequenceNormalization
The AbstractProbeSequenceNormalization class
The ChipEffectSet class
AdditiveCovariatesNormalization
The AdditiveCovariatesNormalization class
The AffymetrixPgfFile class
The AffymetrixProbeTabFile class
The BaseCountNormalization class
The ChipEffectTransform class
The CnPlm class
BasePositionNormalization
The BasePositionNormalization class
The CnProbeAffinityFile class
The FirmaFile class
The FirmaModel class
The FirmaSet class
The AffymetrixCelFile class
The AffymetrixCelSet class
FragmentEquivalentClassNormalization
The FragmentEquivalentClassNormalization class
The MbeiPlm class
The AvgCnPlm class
The AvgPlm class
The ExonProbeAffinityFile class
The DChipCdfBinFile class
The CnagCfhFile class
The CnagCfhSet class
The DChipDcpSet class
The DChipDcpFile class
The ExonRmaPlm class
The AffymetrixFileSet class
AffymetrixFileSetReporter
The AffymetrixFileSetReporter class
The DChipGenomeInformation class
The CnChipEffectFile class
The CnChipEffectSet class
FragmentLengthNormalization
The FragmentLengthNormalization class
LinearModelProbeSequenceNormalization
The LinearModelProbeSequenceNormalization class
The MbeiSnpPlm class
The GcContentNormalization class
DChipQuantileNormalization
The DChipQuantileNormalization class
The ProbeLevelTransform3 class
The HetLogAddCnPlm class
The HetLogAddPlm class
The MatNormalization class
The Model class
Non-documented objects
The ParameterCelSet class
The QualityAssessmentFile class
The ProbeAffinityFile class
The QualityAssessmentModel class
The MultiArrayUnitModel class
The QualityAssessmentSet class
The QuantileNormalization class
The RmaBackgroundCorrection class
The SnpChipEffectGroupMerge class
ReseqCrosstalkCalibration
The ReseqCrosstalkCalibration class
The SingleArrayUnitModel class
The RmaCnPlm class
The DChipSnpInformation class
The ScaleNormalization class
The SmoothMultiarrayModel class
The GcContentNormalization2 class
The SnpChipEffectSet class
GcRmaBackgroundCorrection
The GcRmaBackgroundCorrection class
The WeightsFile class
NormExpBackgroundCorrection
The NormExpBackgroundCorrection class
The SmoothRmaModel class
The ScaleNormalization3 class
The SnpChipEffectFile class
The WeightsSet class
The TransformReport class
The SnpProbeAffinityFile class
The HetLogAddSnpPlm class
LimmaBackgroundCorrection
The LimmaBackgroundCorrection class
The SpatialReporter class
averageQuantile.AffymetrixCelSet
Calculates the average empirical distribution across all samples
OpticalBackgroundCorrection
The OpticalBackgroundCorrection class
Creates a CDF from tiling-array BPMAP file
as.character.AffymetrixCelSet
Returns a short string describing the Affymetrix CEL set
as.character.AffymetrixCnChpSet
Returns a short string describing the set
The ParameterCelFile class
The RmaPlm class
AffymetrixCelFile$clearData
Clears all or a subset of the fields in a CEL file
Coerce an object to an CnagCfhSet object
The UgpGenomeInformation class
as.DChipDcpSet.DChipDcpSet
Coerce an object to an DChipDcpSet object
The RmaSnpPlm class
compare.AffymetrixCdfFile
Checks if two AffymetrixCdfFile objects are equal
byChipType.DChipSnpInformation
Defines a DChipSnpInformation object by chip type
GenomeInformation$byChipType
Static method to define a genome information set by chip type
The SnpInformation class
The SnpPlm interface class
Package aroma.affymetrix
as.AffymetrixCelSet.AffymetrixCelSet
Coerce an object to an AffymetrixCelSet object
AffymetrixCelFile$allocateFromCdf
Creates an empty CEL file from a template CDF
createUniqueCdf.AffymetrixCdfFile
Creates a unique-cell version of the CDF
The AffineSnpPlm class
Defines an AffymetrixFileSet object by searching for Affymetrix files
The AffymetrixCdfFile class
AromaUnitTabularBinaryFile$allocateFromCdf
Creates an AromaUnitTabularBinaryFile mapping to a given CDF
Estimation and assessment of raw copy numbers at the single locus level (CRMA v1)
calculateBaseline.ChipEffectSet
Estimates the baseline signal chromosome by chromosome
createFrom.AffymetrixCelFile
Creates a CEL file using another as a template
createMonocellCdf.AffymetrixCdfFile
Creates a mono-cell version of the CDF
calculateParametersGsb.AffymetrixCelSet
Computes parameters for adjustment of specific binding
AffymetrixCelFile$fromFile
Defines an AffymetrixCelFile object from a CEL file
The AlleleSummation class
AromaChipTypeAnnotationFile$byChipType
Defines an AromaChipTypeAnnotationFile object by chip type
AffymetrixPgfFile$fromFile
Defines an AffymetrixPgfFile object from a PGF file
as.AffymetrixCnChpSet.AffymetrixCnChpSet
Coerce an object to an AffymetrixCnChpSet object
byChipType.DChipGenomeInformation
Defines a DChipGenomeInformation object by chip type
as.AffymetrixFileSet.AffymetrixFileSet
Coerce an object to an AffymetrixFileSet object
extractExpressionSet.ChipEffectSet
Extracts an in-memory ExpressionSet object
Gets the CDF structure for this CEL file
calculateResidualSet.FirmaModel
Gets the set of residuals corresponding to the PLM
Gets the CDF structure for this CEL set
Robust Multichip Analysis (GCRMA)
extractMatrix.AffymetrixCelSet
Extract data as a matrix for a set of arrays
extractMatrix.ParameterCelSet
Extract data as a matrix for a set of arrays
byChipType.SnpInformation
Static method to define a genome information set by chip type
AllelicCrosstalkCalibration
The AllelicCrosstalkCalibration class
UgpGenomeInformation$byChipType
Defines a UgpGenomeInformation object by chip type
convertUnits.AffymetrixCdfFile
Gets and validates unit indices
The ChipEffectFile class
getCellIndices.CnProbeAffinityFile
Retrieves tree list of cell indices for a set of units
The ChipEffectGroupMerge class
ChipEffectFile$fromDataFile
Retrieve an existing CEL file, or create from CDF template if missing
The CrlmmParametersFile class
createExonByTranscriptCdf.AffymetrixCdfFile
Creates an exon-by-transcript CDF
getCellIndices.ExonChipEffectFile
Retrieves tree list of cell indices for a set of units
AffymetrixCdfFile$fromFile
Defines an AffymetrixCdfFile object from a CDF file
extractFeatureSet.AffymetrixCelSet
Extracts CEL signals an in-memory FeatureSet object
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays (CRMA v2)
Robust Multichip Analysis (RMA)
findByChipType.AromaChipTypeAnnotationFile
Locates an annotation file by its chip type
getChipType.SnpInformation
Gets the chip type of this genome information set
The CrlmmParametersSet class
getCnNames.AffymetrixCdfFile
Gets the names of the CN units
Gets the alias of the report
Gets the name alias for the model
Estimates the model parameters
The ExonChipEffectFile class
Estimates the model parameters
getData.GenomeInformation
Gets all or a subset of the genome information data
Identifies non-fitted units
Gets all or a subset of the genome information data
Gets the input data set for this model
Gets the set of FIRMA results for this model
The ExonChipEffectSet class
getHeader.AffymetrixCdfFile
Gets the header of the CDF file
The GenericReporter class
getFitUnitGroupFunction.AffinePlm
Gets the low-level function that fits the PLM
Finding Isoforms using Robust Multichip Analysis (FIRMA)
The GenomeInformation class
The MatSmoothing class
getHeader.AffymetrixCelFile
Gets the header of the CEL file
findUnitsTodo.ProbeLevelModel
Identifies non-fitted units
getOutputDataSet.TransformReport
Gets the transformed data set
Identifies non-fitted units
Gets the path of this model
getProbeAffinityFile.ProbeLevelModel
Gets the probe affinities for this model
getResiduals.QualityAssessmentModel
Calculates the residuals from a probe-level model
getAlleleProbePairs3.AffymetrixCdfFile
Gets the indices of probepairs with the same pair of SNP nucleotides
fit.SmoothMultiarrayModel
Fits the model for one chromosome across samples
getFitUnitGroupFunction.AvgPlm
Gets the low-level function that fits the PLM
getFullName.TransformReport
Gets the full name of the output data set
getGenomeInformation.AffymetrixCdfFile
Gets genome information for this chip type
Gets the header of the CEL file
getAverageFile.AffymetrixCelSet
Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set
The MbeiCnPlm class
getImage.AffymetrixCelFile
Creates an RGB Image object from a CEL file
The ProbeLevelModel class
Gets the tags of the reporter
Gets the tags of the output data set
fitQuantileNormFcn.AffymetrixCelFile
Fits quantile normalization functions for the arrays in the data set
getAlleleCellPairs.AffymetrixCdfFile
Gets the cell indices of allele pairs
Gets the CDF structure for this CEL file
getUnitGroupCellMap.ChipEffectFile
Gets a (unit, group, cell) index map
GenomeInformation$fromCdf
Static method to define a genome information set from a CDF
image270.AffymetrixCelFile
Displays all or a subset of the data spatially
getWeights.QualityAssessmentModel
Calculates the weights from the robust fit to a probe-level model
Gets the CDF structure for this CFH set
Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
getCellIndices.ExonProbeAffinityFile
Retrieves tree list of cell indices for a set of units
The ProbeLevelTransform class
getAlleleProbePairs.AffymetrixCdfFile
Gets the indices of probepairs with the same pair of SNP nucleotides
The ResidualFile class
Retrieves tree list of cell indices for a set of units
Static method to define a genome information set from a CDF
getAverageFile.CnagCfhSet
Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CFH set
getUnitIndices.GenomeInformation
Gets unit indices ordered along the chromosome
getBaseline.ChipEffectSet
Gets the baseline signals across chromosomes
AromaChipTypeAnnotationFile$fromFile
Sets up an AromaChipTypeAnnotationFile
getCellIndices.ProbeAffinityFile
Retrieves tree list of cell indices for a set of units
The ResidualSet class
Gets the chip type for this CEL file
getDataSet.AffymetrixCelSetReporter
Gets the data set
The UnitModel class
Checks which cells (probes) are PMs and not
getChipType.GenomeInformation
Gets the chip type of this genome information set
getCellIndices.ResidualFile
Retrieves tree list of cell indices for a set of units
process.DChipQuantileNormalization
Normalizes the data set
isResequenceChip.AffymetrixCdfFile
Static method to check if a CDF is for a resequencing (CustomSeq) chip
getFitUnitGroupFunction.ExonRmaPlm
Gets the low-level function that fits the Exon PLM
writeImage.AffymetrixCelFile
Writes a spatial image of the signals in the CEL file
CnChipEffectSet$importFromApt
Imports copy-number estimates from an APT summary file
Processes the data set
getChipEffectSet.AlleleSummation
Gets the set of chip effects for this model
Plots a (merged or non-merged) list of boxplot.stats() elements
UnitTypeScaleNormalization
The UnitTypeScaleNormalization class
getChipEffectSet.ProbeLevelModel
Gets the set of chip effects for this model
Gets the full name of the output set
Returns a short string describing the CNAG CFH set
Gets the data set
Defines an CnagCfhFile object from a CFH file
getCellIndices.ChipEffectFile
Retrieves tree list of cell indices for a set of units
getCellIndices.CnChipEffectFile
Retrieves tree list of cell indices for a set of units
Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type
process.OpticalBackgroundCorrection
Performs background correction
process.AbstractProbeSequenceNormalization
Normalizes the data set
Verifies the correctness of the underlying file
isSnpChip.AffymetrixCdfFile
Static method to check if a chip is a mapping (SNP) chip
Returns a short string describing the DChip CHP set
process.FragmentEquivalentClassNormalization
Normalizes the data set
SingleArrayUnitModel$getFitUnitGroupFunction
Static method to get the low-level function that fits the PLM
readRawData.AffymetrixCelFile
Gets all or a subset of the fields in a CEL file
process.UnitTypeScaleNormalization
Normalizes the data set
getFitUnitGroupFunction.FirmaModel
Static method to get the low-level function that fits the PLM
computeAffinities.AffymetrixCdfFile
Calculates probe affinities from sequence
Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
Gets the path of the output data set
getUnitNames.AffymetrixCdfFile
Gets the names of each unit
Gets the cell indices unit by unit
getInputDataSet.TransformReport
Gets the source data set
Gets the name of the explorer
getCellIndices.WeightsFile
Retrieves tree list of cell indices for a set of units
Sets the CDF structure for this CEL file
getFitUnitGroupFunction.RmaPlm
Gets the low-level function that fits the PLM
getIntensities.AffymetrixCelSet
Gets cell intensities from a set of cells and a set of arrays
Sets and resets the .Random.seed in the global environment
Generates an Affymetrix CDF file from a Platform Design (PD) package
getPositions.GenomeInformation
Gets the physical positions for a set of units
plotMvsA.AffymetrixCelFile
Plots log-ratio versus log-intensity in a scatter plot
convert.AffymetrixCdfFile
Converts a CDF into the same CDF but with another format
getFitUnitGroupFunction.HetLogAddPlm
Gets the low-level function that fits the PLM
process.FragmentLengthNormalization
Normalizes the data set
Gets the tags of the output data set
Sets the CDF structure for this CEL file
getFitUnitGroupFunction.MbeiPlm
Gets the low-level function that fits the PLM
plotMvsX.AffymetrixCelFile
Plots log-ratio versus another variable in a scatter plot
getTimestamp.AffymetrixCelFile
Gets the timestamp in the CEL header
process.GcContentNormalization
Normalizes the data set
getUnitTypes.AffymetrixCdfFile
Gets the types of a set of units
groupUnitsByDimension.AffymetrixCdfFile
Groups units by dimensions
process.ScaleNormalization3
Normalizes the data set
getUnitIntensities.AffymetrixCelSet
Gets cell signals for a subset of units and a subset of arrays
MultiArrayUnitModel$getFitUnitGroupFunction
Static method to get the low-level function that fits the PLM
Sets the CDF structure for this CEL set
getUnitNames.AffymetrixPgfFile
Gets the names of each unit
extractAffyBatch.AffymetrixCelSet
Extracts an in-memory AffyBatch object from the CEL set
plotDensity.AffymetrixCelFile
Plots the density of the probe signals on the array
process.AdditiveCovariatesNormalization
Normalizes the data set
readUnits.MultiArrayUnitModel
Reads data unit by unit
extractDataFrame.ParameterCelSet
Extract data as a data.frame for a set of arrays
isDuplicated.AffymetrixCelSet
Identifies duplicated CEL files
Gets the name of the output data set
Robust Multichip Analysis (RMA) reproducing the affy package
AffymetrixCdfFile$findByChipType
Locates a CDF file from its chip type
Generates image files, scripts and dynamic pages for the explorer
process.AllelicCrosstalkCalibration
Calibrates the data set
Identifies duplicated CFH files
AffymetrixPgfFile$findByChipType
Locates a PGF file from its chip type
updateUnits.AffymetrixCelFile
Updates CEL data unit by unit
Sets the name alias for the model
Estimates the model parameters
Gets the root path of this model
Generates image files, scripts and dynamic pages for the explorer
getSnpNames.AffymetrixCdfFile
Gets the names of the SNP units
Estimates the model parameters
normalizeQuantile.AffymetrixCelFile
Normalizes the probe intensities to a target empirical distribution
Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file
Gets the log-intensities and log-ratios of chip effects for two arrays
Gets the CDF structure for this model
Generates report
Sets the arrays
normalizeQuantile.AffymetrixCelSet
Normalizes samples to have the same empirical distribution
process.LimmaBackgroundCorrection
Performs background correction
plotDensity.GenomeInformation
Plots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFile
Displays a spatial plot of a CEL file
Gets the name of the output data set
getCellIndices.AffymetrixCdfFile
Gets the cell indices unit by unit
process.GcRmaBackgroundCorrection
Performs background correction
getCellIndices.SnpChipEffectFile
Retrieves tree list of cell indices for a set of units
getCellIndices.SnpProbeAffinityFile
Retrieves tree list of cell indices for a set of units
nbrOfGroupsPerUnit.AffymetrixCdfFile
Gets the number of groups in each unit
Sets the alias of the report
Sets the CDF structure for this CFH set
getChipType.AffymetrixCelFile
Gets the chip type for this CEL file
getChipType.AffymetrixCelSet
Gets the chip type for this CEL set
Verifies the correctness of the underlying file
process.QuantileNormalization
Normalizes the data set
AffymetrixCelSet$importFromDChip
Imports dChip-exported CEL files
CnChipEffectSet$importFromDChip
Imports copy-number estimates from a dChip result file
getHeader.AffymetrixPgfFile
Gets the header of the PGF file
readUnits.AffymetrixCdfFile
Reads CDF data unit by unit
getHeader.AromaChipTypeAnnotationFile
Gets the header of the annotation file
process.ReseqCrosstalkCalibration
Calibrates the data set
plotDensity.AffymetrixCelSet
Plots the densities of all samples
readUnitsByQuartets.AffymetrixCdfFile
Gets the cell quartets for each base position
Normalizes the data set
process.ScaleNormalization
Normalizes the data set
getOutputDataSet.Transform
Gets the transformed data set
process.RmaBackgroundCorrection
Performs background correction
nbrOfSnps.AffymetrixCdfFile
Gets the number of SNPs
Sets the tags to be appended
readUnits.SingleArrayUnitModel
Reads data unit by unit
process.BackgroundCorrection
Processes the data set
setRestructor.AffymetrixCdfFile
Specifies a function through which
process.ChipEffectGroupMerge
Normalizes the data set
readUnits.AffymetrixCelFile
Reads CEL data unit by unit
setupExampleData.AromaAffymetrix
Setups example data in the current directory
Reads CEL data unit by unit
smoothScatterMvsA.AffymetrixCelFile
Plots log-ratio versus log-intensity in a smooth scatter plot