Analysis of Large Affymetrix Microarray Data Sets
Normalizes the data set
Normalizes the data set
Normalizes the data set
Normalizes the data set
Normalizes the data set
Performs background correction
Generates report
Performs background correction
Normalizes the data set
Processes the data set
Performs background correction
Calibrates the data set
Performs background correction
Normalizes the data set
Normalizes the data set
Generates image files, scripts and dynamic pages for the explorer
Normalizes the data set
The QualityAssessmentFile class
The QualityAssessmentModel class
The QualityAssessmentSet class
The QuantileNormalization class
Sets and resets the .Random.seed in the global environment
Gets all or a subset of the fields in a CEL file
Reads CDF data unit by unit
Reads CEL data unit by unit
Reads CEL data unit by unit
Reads data unit by unit
Reads data unit by unit
Gets the cell quartets for each base position
The AbstractProbeSequenceNormalization class
The AdditiveCovariatesNormalization class
The AffineCnPlm class
The AffinePlm class
The AffineSnpPlm class
The AffymetrixCdfFile class
The AffymetrixCelFile class
The AffymetrixCelSet class
The AffymetrixCelSetReporter class
The AffymetrixCelSetTuple class
The AffymetrixCnChpSet class
The abstract AffymetrixFile class
The AffymetrixFileSet class
The AffymetrixFileSetReporter class
The AffymetrixPgfFile class
The AffymetrixProbeTabFile class
The AlleleSummation class
The AllelicCrosstalkCalibration class
Creates an empty CEL file from a template CDF
Creates an AromaUnitTabularBinaryFile mapping to a given CDF
Package aroma.affymetrix
The AromaChipTypeAnnotationFile class
The ArrayExplorer class
Coerce an object to an AffymetrixCelSet object
Coerce an object to an AffymetrixCnChpSet object
Coerce an object to an AffymetrixFileSet object
Returns a short string describing the Affymetrix CEL set
Returns a short string describing the set
Returns a short string describing the CNAG CFH set
Returns a short string describing the DChip CHP set
Coerce an object to an CnagCfhSet object
Coerce an object to an DChipDcpSet object
Calculates the average empirical distribution across all samples
The AvgCnPlm class
The AvgPlm class
The AvgSnpPlm class
The BackgroundCorrection class
The BaseCountNormalization class
The BasePositionNormalization class
Creates a CDF from tiling-array BPMAP file
Defines an AromaChipTypeAnnotationFile object by chip type
Defines a DChipGenomeInformation object by chip type
Defines a DChipSnpInformation object by chip type
Static method to define a genome information set by chip type
Static method to define a genome information set by chip type
Defines a UgpGenomeInformation object by chip type
Defines an AffymetrixFileSet object by searching for Affymetrix files
Estimates the baseline signal chromosome by chromosome
Computes parameters for adjustment of specific binding
Gets the set of residuals corresponding to the PLM
The ChipEffectFile class
The ChipEffectGroupMerge class
The ChipEffectSet class
The ChipEffectTransform class
Clears all or a subset of the fields in a CEL file
The CnagCfhFile class
The CnagCfhSet class
The CnChipEffectFile class
The CnChipEffectSet class
The CnPlm class
The CnProbeAffinityFile class
Checks if two AffymetrixCdfFile objects are equal
Calculates probe affinities from sequence
Converts a CDF into the same CDF but with another format
Gets and validates unit indices
Creates an exon-by-transcript CDF
Creates a CEL file using another as a template
Creates a mono-cell version of the CDF
Creates a unique-cell version of the CDF
The CrlmmParametersFile class
The CrlmmParametersSet class
The DChipCdfBinFile class
The DChipDcpFile class
The DChipDcpSet class
The DChipGenomeInformation class
The DChipQuantileNormalization class
The DChipSnpInformation class
Estimation and assessment of raw copy numbers at the single locus leve...
A single-array preprocessing method for estimating full-resolution raw...
Finding Isoforms using Robust Multichip Analysis (FIRMA)
Robust Multichip Analysis (GCRMA)
Robust Multichip Analysis (RMA)
The ExonChipEffectFile class
The ExonChipEffectSet class
The ExonProbeAffinityFile class
The ExonRmaPlm class
Extracts an in-memory AffyBatch object from the CEL set
Extract data as a data.frame for a set of arrays
Extracts an in-memory ExpressionSet object
Extracts CEL signals an in-memory FeatureSet object
Extract data as a matrix for a set of arrays
Extract data as a matrix for a set of arrays
Locates a CDF file from its chip type
Locates a PGF file from its chip type
Locates an annotation file by its chip type
Identifies non-fitted units
Identifies non-fitted units
Identifies non-fitted units
The FirmaFile class
The FirmaModel class
The FirmaSet class
Estimates the model parameters
Estimates the model parameters
Estimates the model parameters
Estimates the model parameters
Fits the model for one chromosome across samples
Fits quantile normalization functions for the arrays in the data set
The FragmentEquivalentClassNormalization class
The FragmentLengthNormalization class
Static method to define a genome information set from a CDF
Static method to define a genome information set from a CDF
Retrieve an existing CEL file, or create from CDF template if missing
Defines an AffymetrixCdfFile object from a CDF file
Defines an AffymetrixCelFile object from a CEL file
Defines an AffymetrixPgfFile object from a PGF file
Sets up an AromaChipTypeAnnotationFile
Defines an CnagCfhFile object from a CFH file
The GcContentNormalization class
The GcContentNormalization2 class
The GcRmaBackgroundCorrection class
The GenericReporter class
The GenomeInformation class
Gets the alias of the report
Gets the name alias for the model
Gets the cell indices of allele pairs
Gets the indices of probepairs with the same pair of SNP nucleotides
Gets the indices of probepairs with the same pair of SNP nucleotides
Gets the log-intensities and log-ratios of chip effects for two arrays
Gets the log-intensities and log-ratios of chip effects of the set rel...
Calculates the mean and the standard deviation of the cell signal (int...
Calculates the mean and the standard deviation of the cell signal (int...
Gets the baseline signals across chromosomes
Gets the CDF structure for this CEL file
Gets the CDF structure for this CEL set
Gets the CDF structure for this CEL file
Gets the CDF structure for this CFH set
Gets the CDF structure for this model
Gets the cell indices unit by unit
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Retrieves tree list of cell indices for a set of units
Gets the cell indices unit by unit
Retrieves tree list of cell indices for a set of units
Gets the set of chip effects for this model
Gets the set of chip effects for this model
Gets the chip type for this CEL file
Gets the chip type for this CEL set
Gets the chip type for this CEL file
Gets the chip type of this genome information set
Gets the chip type of this genome information set
Gets the names of the CN units
Gets all or a subset of the genome information data
Gets all or a subset of the genome information data
Gets the data set
Gets the data set
Gets the input data set for this model
Gets the set of FIRMA results for this model
Gets the low-level function that fits the PLM
Gets the low-level function that fits the PLM
Gets the low-level function that fits the Exon PLM
Static method to get the low-level function that fits the PLM
Gets the low-level function that fits the PLM
Gets the low-level function that fits the PLM
Static method to get the low-level function that fits the PLM
Gets the low-level function that fits the PLM
Static method to get the low-level function that fits the PLM
Gets the full name of the output set
Gets the full name of the output data set
Gets genome information for this chip type
Gets the header of the CDF file
Gets the header of the CEL file
Gets the header of the PGF file
Gets the header of the annotation file
Gets the header of the CEL file
Creates an RGB Image object from a CEL file
Gets the source data set
Gets cell intensities from a set of cells and a set of arrays
Gets the name of the explorer
Gets the name of the output data set
Gets the name of the output data set
Gets the transformed data set
Gets the transformed data set
Gets the path of this model
Gets the path of the output data set
Gets the physical positions for a set of units
Gets the probe affinities for this model
Calculates the residuals from a probe-level model
Gets the root path of this model
Gets the names of the SNP units
Gets the tags of the reporter
Gets the tags of the output data set
Gets the tags of the output data set
Gets the timestamp in the CEL header
Gets a (unit, group, cell) index map
Gets unit indices ordered along the chromosome
Gets cell signals for a subset of units and a subset of arrays
Gets the names of each unit
Gets the names of each unit
Gets the types of a set of units
Calculates the weights from the robust fit to a probe-level model
Gets the physical position, log-intensities and log-ratios of chip eff...
Gets the physical position, log-intensities and log-ratios of chip eff...
Groups units by dimensions
The HetLogAddCnPlm class
The HetLogAddPlm class
The HetLogAddSnpPlm class
Displays all or a subset of the data spatially
Imports copy-number estimates from an APT summary file
Imports dChip-exported CEL files
Imports copy-number estimates from a dChip result file
Identifies duplicated CEL files
Identifies duplicated CFH files
Checks which cells (probes) are PMs and not
Static method to check if a CDF is for a resequencing (CustomSeq) chip
Static method to check if a chip is a mapping (SNP) chip
Robust Multichip Analysis (RMA) reproducing the affy package
The LimmaBackgroundCorrection class
The LinearModelProbeSequenceNormalization class
The MatNormalization class
The MatSmoothing class
The MbeiCnPlm class
The MbeiPlm class
The MbeiSnpPlm class
The Model class
The MultiArrayUnitModel class
Gets the number of groups in each unit
Gets the number of SNPs
Non-documented objects
Normalizes the probe intensities to a target empirical distribution
Normalizes samples to have the same empirical distribution
The NormExpBackgroundCorrection class
The OpticalBackgroundCorrection class
The ParameterCelFile class
The ParameterCelSet class
Generates an Affymetrix CDF file from a Platform Design (PD) package a...
Plots a (merged or non-merged) list of boxplot.stats() elements
Plots the density of the probe signals on the array
Plots the densities of all samples
Plots the density of SNPs for a given chromosome
Displays a spatial plot of a CEL file
Plots log-ratio versus log-intensity in a scatter plot
Plots log-ratio versus another variable in a scatter plot
The ProbeAffinityFile class
The ProbeLevelModel class
The ProbeLevelTransform class
The ProbeLevelTransform3 class
Normalizes the data set
Normalizes the data set
Calibrates the data set
Generates image files, scripts and dynamic pages for the explorer
Processes the data set
Normalizes the data set
The ReseqCrosstalkCalibration class
The ResidualFile class
The ResidualSet class
The RmaBackgroundCorrection class
The RmaCnPlm class
The RmaPlm class
The RmaSnpPlm class
The ScaleNormalization class
The ScaleNormalization3 class
Sets the alias of the report
Sets the name alias for the model
Sets the arrays
Sets the CDF structure for this CEL file
Sets the CDF structure for this CEL set
Sets the CDF structure for this CEL file
Sets the CDF structure for this CFH set
Specifies a function through which
Sets the tags to be appended
Setups example data in the current directory
The SingleArrayUnitModel class
The SmoothMultiarrayModel class
The SmoothRmaModel class
Plots log-ratio versus log-intensity in a smooth scatter plot
The SnpChipEffectFile class
The SnpChipEffectGroupMerge class
The SnpChipEffectSet class
The SnpInformation class
The SnpPlm interface class
The SnpProbeAffinityFile class
The SpatialReporter class
The TransformReport class
The UgpGenomeInformation class
The UnitModel class
The UnitTypeScaleNormalization class
Updates CEL data unit by unit
Verifies the correctness of the underlying file
Verifies the correctness of the underlying file
The WeightsFile class
The WeightsSet class
Generates an Affymetrix CDF file from a Platform Design (PD) package
Writes a spatial image of the signals in the CEL file
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
Useful links