Man pages for aroma.affymetrix
Analysis of Large Affymetrix Microarray Data Sets
| 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 |
| AffymetrixProbeTabFile | The AffymetrixProbeTabFile class |
| AlleleSummation | The AlleleSummation class |
| AllelicCrosstalkCalibration | The AllelicCrosstalkCalibration class |
| allocateFromCdf.AffymetrixCelFile | Creates an empty CEL file from a template CDF |
| allocateFromCdf.AromaUnitTabularBinaryFile | Creates an AromaUnitTabularBinaryFile mapping to a given CDF |
| aroma.affymetrix-package | Package aroma.affymetrix |
| AromaChipTypeAnnotationFile | The AromaChipTypeAnnotationFile class |
| ArrayExplorer | The ArrayExplorer class |
| as.AffymetrixCelSet.AffymetrixCelSet | Coerce an object to an AffymetrixCelSet object |
| as.AffymetrixCnChpSet.AffymetrixCnChpSet | Coerce an object to an AffymetrixCnChpSet object |
| as.AffymetrixFileSet.AffymetrixFileSet | Coerce an object to an AffymetrixFileSet object |
| as.character.AffymetrixCelSet | Returns a short string describing the Affymetrix CEL set |
| as.character.AffymetrixCnChpSet | Returns a short string describing the set |
| as.character.CnagCfhSet | Returns a short string describing the CNAG CFH set |
| as.character.DChipDcpSet | Returns a short string describing the DChip CHP set |
| as.CnagCfhSet.CnagCfhSet | Coerce an object to an CnagCfhSet object |
| as.DChipDcpSet.DChipDcpSet | Coerce an object to an DChipDcpSet object |
| averageQuantile.AffymetrixCelSet | Calculates the average empirical distribution across all... |
| AvgCnPlm | The AvgCnPlm class |
| AvgPlm | The AvgPlm class |
| AvgSnpPlm | The AvgSnpPlm class |
| BackgroundCorrection | The BackgroundCorrection class |
| BaseCountNormalization | The BaseCountNormalization class |
| BasePositionNormalization | The BasePositionNormalization class |
| bpmapCluster2Cdf | Creates a CDF from tiling-array BPMAP file |
| byChipType.AromaChipTypeAnnotationFile | Defines an AromaChipTypeAnnotationFile object by chip type |
| byChipType.DChipGenomeInformation | Defines a DChipGenomeInformation object by chip type |
| byChipType.DChipSnpInformation | Defines a DChipSnpInformation object by chip type |
| byChipType.GenomeInformation | Static method to define a genome information set by chip type |
| byChipType.SnpInformation | Static method to define a genome information set by chip type |
| byChipType.UgpGenomeInformation | Defines a UgpGenomeInformation object by chip type |
| byPath.AffymetrixFileSet | Defines an AffymetrixFileSet object by searching for... |
| calculateBaseline.ChipEffectSet | Estimates the baseline signal chromosome by chromosome |
| calculateParametersGsb.AffymetrixCelSet | Computes parameters for adjustment of specific binding |
| calculateResidualSet.FirmaModel | Gets the set of residuals corresponding to the PLM |
| ChipEffectFile | The ChipEffectFile class |
| ChipEffectGroupMerge | The ChipEffectGroupMerge class |
| ChipEffectSet | The ChipEffectSet class |
| ChipEffectTransform | The ChipEffectTransform class |
| clearData.AffymetrixCelFile | Clears all or a subset of the fields in a CEL file |
| CnagCfhFile | The CnagCfhFile class |
| CnagCfhSet | The CnagCfhSet class |
| CnChipEffectFile | The CnChipEffectFile class |
| CnChipEffectSet | The CnChipEffectSet class |
| CnPlm | The CnPlm class |
| CnProbeAffinityFile | The CnProbeAffinityFile class |
| compare.AffymetrixCdfFile | Checks if two AffymetrixCdfFile objects are equal |
| computeAffinities.AffymetrixCdfFile | Calculates probe affinities from sequence |
| convert.AffymetrixCdfFile | Converts a CDF into the same CDF but with another format |
| convertUnits.AffymetrixCdfFile | Gets and validates unit indices |
| createExonByTranscriptCdf.AffymetrixCdfFile | Creates an exon-by-transcript CDF |
| createFrom.AffymetrixCelFile | Creates a CEL file using another as a template |
| createMonocellCdf.AffymetrixCdfFile | Creates a mono-cell version of the CDF |
| createUniqueCdf.AffymetrixCdfFile | Creates a unique-cell version of the CDF |
| 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 |
| doCRMAv1 | Estimation and assessment of raw copy numbers at the single... |
| doCRMAv2 | A single-array preprocessing method for estimating... |
| doFIRMA | Finding Isoforms using Robust Multichip Analysis (FIRMA) |
| doGCRMA | Robust Multichip Analysis (GCRMA) |
| doRMA | Robust Multichip Analysis (RMA) |
| ExonChipEffectFile | The ExonChipEffectFile class |
| ExonChipEffectSet | The ExonChipEffectSet class |
| ExonProbeAffinityFile | The ExonProbeAffinityFile class |
| ExonRmaPlm | The ExonRmaPlm class |
| extractAffyBatch.AffymetrixCelSet | Extracts an in-memory AffyBatch object from the CEL set |
| extractDataFrame.ParameterCelSet | Extract data as a data.frame for a set of arrays |
| extractExpressionSet.ChipEffectSet | Extracts an in-memory ExpressionSet object |
| extractFeatureSet.AffymetrixCelSet | Extracts CEL signals an in-memory FeatureSet object |
| extractMatrix.AffymetrixCelSet | Extract data as a matrix for a set of arrays |
| extractMatrix.ParameterCelSet | Extract data as a matrix for a set of arrays |
| findByChipType.AffymetrixCdfFile | Locates a CDF file from its chip type |
| findByChipType.AffymetrixPgfFile | Locates a PGF file from its chip type |
| findByChipType.AromaChipTypeAnnotationFile | Locates an annotation file by its chip type |
| findUnitsTodo.FirmaModel | Identifies non-fitted units |
| findUnitsTodo.ProbeLevelModel | Identifies non-fitted units |
| findUnitsTodo.UnitModel | Identifies non-fitted units |
| FirmaFile | The FirmaFile class |
| FirmaModel | The FirmaModel class |
| FirmaSet | The FirmaSet class |
| fit.FirmaModel | Estimates the model parameters |
| fit.Model | Estimates the model parameters |
| fit.ProbeLevelModel | Estimates the model parameters |
| fitQuantileNormFcn.AffymetrixCelFile | Fits quantile normalization functions for the arrays in the... |
| fit.SingleArrayUnitModel | Estimates the model parameters |
| fit.SmoothMultiarrayModel | Fits the model for one chromosome across samples |
| FragmentEquivalentClassNormalization | The FragmentEquivalentClassNormalization class |
| FragmentLengthNormalization | The FragmentLengthNormalization class |
| fromCdf.GenomeInformation | Static method to define a genome information set from a CDF |
| fromCdf.SnpInformation | Static method to define a genome information set from a CDF |
| fromDataFile.ChipEffectFile | Retrieve an existing CEL file, or create from CDF template if... |
| fromFile.AffymetrixCdfFile | Defines an AffymetrixCdfFile object from a CDF file |
| fromFile.AffymetrixCelFile | Defines an AffymetrixCelFile object from a CEL file |
| fromFile.AffymetrixPgfFile | Defines an AffymetrixPgfFile object from a PGF file |
| fromFile.AromaChipTypeAnnotationFile | Sets up an AromaChipTypeAnnotationFile |
| fromFile.CnagCfhFile | Defines an CnagCfhFile object from a CFH file |
| GcContentNormalization | The GcContentNormalization class |
| GcContentNormalization2 | The GcContentNormalization2 class |
| GcRmaBackgroundCorrection | The GcRmaBackgroundCorrection class |
| GenericReporter | The GenericReporter class |
| GenomeInformation | The GenomeInformation class |
| getAlias.GenericReporter | Gets the alias of the report |
| getAlias.Model | Gets the name alias for the model |
| getAlleleCellPairs.AffymetrixCdfFile | Gets the cell indices of allele pairs |
| getAlleleProbePairs3.AffymetrixCdfFile | Gets the indices of probepairs with the same pair of SNP... |
| getAlleleProbePairs.AffymetrixCdfFile | Gets the indices of probepairs with the same pair of SNP... |
| getAM.ChipEffectFile | Gets the log-intensities and log-ratios of chip effects for... |
| getAM.ChipEffectSet | Gets the log-intensities and log-ratios of chip effects of... |
| getAverageFile.AffymetrixCelSet | Calculates the mean and the standard deviation of the cell... |
| getAverageFile.CnagCfhSet | Calculates the mean and the standard deviation of the cell... |
| getBaseline.ChipEffectSet | Gets the baseline signals across chromosomes |
| getCdf.AffymetrixCelFile | Gets the CDF structure for this CEL file |
| getCdf.AffymetrixCelSet | Gets the CDF structure for this CEL set |
| getCdf.CnagCfhFile | Gets the CDF structure for this CEL file |
| getCdf.CnagCfhSet | Gets the CDF structure for this CFH set |
| getCdf.Model | Gets the CDF structure for this model |
| getCellIndices.AffymetrixCdfFile | Gets the cell indices unit by unit |
| 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 |
| getCellIndices.CnProbeAffinityFile | Retrieves tree list of cell indices for a set of units |
| getCellIndices.ExonChipEffectFile | Retrieves tree list of cell indices for a set of units |
| getCellIndices.ExonProbeAffinityFile | Retrieves tree list of cell indices for a set of units |
| getCellIndices.FirmaFile | Retrieves tree list of cell indices for a set of units |
| getCellIndices.ProbeAffinityFile | Retrieves tree list of cell indices for a set of units |
| getCellIndices.ResidualFile | Retrieves tree list of cell indices for a set of units |
| 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 |
| getCellIndices.UnitModel | Gets the cell indices unit by unit |
| getCellIndices.WeightsFile | Retrieves tree list of cell indices for a set of units |
| getChipEffectSet.AlleleSummation | Gets the set of chip effects for this model |
| getChipEffectSet.ProbeLevelModel | Gets the set of chip effects for this model |
| getChipType.AffymetrixCelFile | Gets the chip type for this CEL file |
| getChipType.AffymetrixCelSet | Gets the chip type for this CEL set |
| getChipType.CnagCfhFile | Gets the chip type for this CEL file |
| getChipType.GenomeInformation | Gets the chip type of this genome information set |
| getChipType.SnpInformation | Gets the chip type of this genome information set |
| getCnNames.AffymetrixCdfFile | Gets the names of the CN units |
| getData.GenomeInformation | Gets all or a subset of the genome information data |
| getDataSet.AffymetrixCelSetReporter | Gets the data set |
| getDataSet.ArrayExplorer | Gets the data set |
| getDataSet.Model | Gets the input data set for this model |
| getData.SnpInformation | Gets all or a subset of the genome information data |
| getFirmaSet.FirmaModel | Gets the set of FIRMA results for this model |
| getFitUnitGroupFunction.AffinePlm | Gets the low-level function that fits the PLM |
| getFitUnitGroupFunction.AvgPlm | Gets the low-level function that fits the PLM |
| getFitUnitGroupFunction.ExonRmaPlm | Gets the low-level function that fits the Exon PLM |
| getFitUnitGroupFunction.FirmaModel | Static method to get the low-level function that fits the PLM |
| getFitUnitGroupFunction.HetLogAddPlm | Gets the low-level function that fits the PLM |
| getFitUnitGroupFunction.MbeiPlm | Gets the low-level function that fits the PLM |
| getFitUnitGroupFunction.MultiArrayUnitModel | Static method to get the low-level function that fits the PLM |
| getFitUnitGroupFunction.RmaPlm | Gets the low-level function that fits the PLM |
| getFitUnitGroupFunction.SingleArrayUnitModel | Static method to get the low-level function that fits the PLM |
| getFullName.Model | Gets the full name of the output set |
| getFullName.TransformReport | Gets the full name of the output data set |
| getGenomeInformation.AffymetrixCdfFile | Gets genome information for this chip type |
| getHeader.AffymetrixCdfFile | Gets the header of the CDF file |
| getHeader.AffymetrixCelFile | Gets the header of the CEL file |
| getHeader.AffymetrixPgfFile | Gets the header of the PGF file |
| getHeader.AromaChipTypeAnnotationFile | Gets the header of the annotation file |
| getHeader.CnagCfhFile | Gets the header of the CEL file |
| getImage.AffymetrixCelFile | Creates an RGB Image object from a CEL file |
| getInputDataSet.TransformReport | Gets the source data set |
| getIntensities.AffymetrixCelSet | Gets cell intensities from a set of cells and a set of arrays |
| getName.GenericReporter | Gets the name of the explorer |
| getName.Model | Gets the name of the output data set |
| getName.TransformReport | Gets the name of the output data set |
| getOutputDataSet.Transform | Gets the transformed data set |
| getOutputDataSet.TransformReport | Gets the transformed data set |
| getPath.Model | Gets the path of this model |
| getPath.TransformReport | Gets the path of the output data set |
| getPositions.GenomeInformation | Gets the physical positions for a set of units |
| getProbeAffinityFile.ProbeLevelModel | Gets the probe affinities for this model |
| getResiduals.QualityAssessmentModel | Calculates the residuals from a probe-level model |
| getRootPath.Model | Gets the root path of this model |
| getSnpNames.AffymetrixCdfFile | Gets the names of the SNP units |
| getTags.GenericReporter | Gets the tags of the reporter |
| getTags.Model | Gets the tags of the output data set |
| getTags.TransformReport | Gets the tags of the output data set |
| getTimestamp.AffymetrixCelFile | Gets the timestamp in the CEL header |
| getUnitGroupCellMap.ChipEffectFile | Gets a (unit, group, cell) index map |
| getUnitIndices.GenomeInformation | Gets unit indices ordered along the chromosome |
| getUnitIntensities.AffymetrixCelSet | Gets cell signals for a subset of units and a subset of... |
| getUnitNames.AffymetrixCdfFile | Gets the names of each unit |
| getUnitNames.AffymetrixPgfFile | Gets the names of each unit |
| getUnitTypes.AffymetrixCdfFile | Gets the types of a set of units |
| getWeights.QualityAssessmentModel | Calculates the weights from the robust fit to a probe-level... |
| getXAM.ChipEffectFile | Gets the physical position, log-intensities and log-ratios of... |
| getXAM.ChipEffectSet | Gets the physical position, log-intensities and log-ratios of... |
| groupUnitsByDimension.AffymetrixCdfFile | Groups units by dimensions |
| HetLogAddCnPlm | The HetLogAddCnPlm class |
| HetLogAddPlm | The HetLogAddPlm class |
| HetLogAddSnpPlm | The HetLogAddSnpPlm class |
| image270.AffymetrixCelFile | Displays all or a subset of the data spatially |
| importFromApt.CnChipEffectSet | Imports copy-number estimates from an APT summary file |
| importFromDChip.AffymetrixCelSet | Imports dChip-exported CEL files |
| importFromDChip.CnChipEffectSet | Imports copy-number estimates from a dChip result file |
| isDuplicated.AffymetrixCelSet | Identifies duplicated CEL files |
| isDuplicated.CnagCfhSet | Identifies duplicated CFH files |
| isPm.AffymetrixCdfFile | Checks which cells (probes) are PMs and not |
| isResequenceChip.AffymetrixCdfFile | Static method to check if a CDF is for a resequencing... |
| isSnpChip.AffymetrixCdfFile | Static method to check if a chip is a mapping (SNP) chip |
| justRMA | Robust Multichip Analysis (RMA) reproducing the affy package |
| 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 |
| nbrOfGroupsPerUnit.AffymetrixCdfFile | Gets the number of groups in each unit |
| nbrOfSnps.AffymetrixCdfFile | Gets the number of SNPs |
| Non-documented_objects | Non-documented objects |
| normalizeQuantile.AffymetrixCelFile | Normalizes the probe intensities to a target empirical... |
| normalizeQuantile.AffymetrixCelSet | Normalizes samples to have the same empirical distribution |
| NormExpBackgroundCorrection | The NormExpBackgroundCorrection class |
| OpticalBackgroundCorrection | The OpticalBackgroundCorrection class |
| ParameterCelFile | The ParameterCelFile class |
| ParameterCelSet | The ParameterCelSet class |
| pdInfo2Cdf | Generates an Affymetrix CDF file from a Platform Design (PD)... |
| plotBoxplotStats.list | Plots a (merged or non-merged) list of boxplot.stats()... |
| plotDensity.AffymetrixCelFile | Plots the density of the probe signals on the array |
| plotDensity.AffymetrixCelSet | Plots the densities of all samples |
| plotDensity.GenomeInformation | Plots the density of SNPs for a given chromosome |
| plotImage.AffymetrixCelFile | Displays a spatial plot of a CEL file |
| plotMvsA.AffymetrixCelFile | Plots log-ratio versus log-intensity in a scatter plot |
| plotMvsX.AffymetrixCelFile | Plots log-ratio versus another variable in a scatter plot |
| ProbeAffinityFile | The ProbeAffinityFile class |
| ProbeLevelModel | The ProbeLevelModel class |
| ProbeLevelTransform | The ProbeLevelTransform class |
| ProbeLevelTransform3 | The ProbeLevelTransform3 class |
| process.AbstractProbeSequenceNormalization | Normalizes the data set |
| process.AdditiveCovariatesNormalization | Normalizes the data set |
| process.AllelicCrosstalkCalibration | Calibrates the data set |
| process.ArrayExplorer | Generates image files, scripts and dynamic pages for the... |
| process.BackgroundCorrection | Processes the data set |
| process.ChipEffectGroupMerge | Normalizes the data set |
| process.DChipQuantileNormalization | Normalizes the data set |
| process.FragmentEquivalentClassNormalization | Normalizes the data set |
| process.FragmentLengthNormalization | Normalizes the data set |
| process.GcContentNormalization | Normalizes the data set |
| process.GcRmaBackgroundCorrection | Performs background correction |
| process.GenericReporter | Generates report |
| process.LimmaBackgroundCorrection | Performs background correction |
| process.MatNormalization | Normalizes the data set |
| process.MatSmoothing | Processes the data set |
| process.OpticalBackgroundCorrection | Performs background correction |
| process.QuantileNormalization | Normalizes the data set |
| process.ReseqCrosstalkCalibration | Calibrates the data set |
| process.RmaBackgroundCorrection | Performs background correction |
| process.ScaleNormalization | Normalizes the data set |
| process.ScaleNormalization3 | Normalizes the data set |
| process.SpatialReporter | Generates image files, scripts and dynamic pages for the... |
| process.UnitTypeScaleNormalization | Normalizes the data set |
| QualityAssessmentFile | The QualityAssessmentFile class |
| QualityAssessmentModel | The QualityAssessmentModel class |
| QualityAssessmentSet | The QualityAssessmentSet class |
| QuantileNormalization | The QuantileNormalization class |
| randomSeed | Sets and resets the .Random.seed in the global environment |
| readRawData.AffymetrixCelFile | Gets all or a subset of the fields in a CEL file |
| readUnits.AffymetrixCdfFile | Reads CDF data unit by unit |
| readUnits.AffymetrixCelFile | Reads CEL data unit by unit |
| readUnitsByQuartets.AffymetrixCdfFile | Gets the cell quartets for each base position |
| readUnits.CnagCfhFile | Reads CEL data unit by unit |
| readUnits.MultiArrayUnitModel | Reads data unit by unit |
| readUnits.SingleArrayUnitModel | Reads data unit by unit |
| 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 |
| setAlias.GenericReporter | Sets the alias of the report |
| setAlias.Model | Sets the name alias for the model |
| setArrays.ArrayExplorer | Sets the arrays |
| setCdf.AffymetrixCelFile | Sets the CDF structure for this CEL file |
| setCdf.AffymetrixCelSet | Sets the CDF structure for this CEL set |
| setCdf.CnagCfhFile | Sets the CDF structure for this CEL file |
| setCdf.CnagCfhSet | Sets the CDF structure for this CFH set |
| setRestructor.AffymetrixCdfFile | Specifies a function through which |
| setTags.Model | Sets the tags to be appended |
| setupExampleData.AromaAffymetrix | Setups example data in the current directory |
| SingleArrayUnitModel | The SingleArrayUnitModel class |
| SmoothMultiarrayModel | The SmoothMultiarrayModel class |
| SmoothRmaModel | The SmoothRmaModel class |
| smoothScatterMvsA.AffymetrixCelFile | Plots log-ratio versus log-intensity in a smooth scatter plot |
| SnpChipEffectFile | The SnpChipEffectFile class |
| SnpChipEffectGroupMerge | The SnpChipEffectGroupMerge 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 |
| updateUnits.AffymetrixCelFile | Updates CEL data unit by unit |
| verify.GenomeInformation | Verifies the correctness of the underlying file |
| verify.SnpInformation | Verifies the correctness of the underlying file |
| WeightsFile | The WeightsFile class |
| WeightsSet | The WeightsSet class |
| writeCdf.AffyGenePDInfo | Generates an Affymetrix CDF file from a Platform Design (PD)... |
| writeImage.AffymetrixCelFile | Writes a spatial image of the signals in the CEL file |
