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Reference index for {aroma.affymetrix}

You are viewing package members beginning with the letter "C"

Function/ClassDescription
calcRawCnStats {aroma.affymetrix}Non-documented objects
calculateBaseline.ChipEffectSet {aroma.affymetrix}Estimates the baseline signal chromosome by chromosome
calculateParametersGsb.AffymetrixCelSet {aroma.affymetrix}Computes parameters for adjustment of specific binding
calculateResidualSet.FirmaModel {aroma.affymetrix}Gets the set of residuals corresponding to the PLM
ChipEffectFile {aroma.affymetrix}The ChipEffectFile class
ChipEffectFile.fromDataFile {aroma.affymetrix}Retrive an existing CEL file, or create from CDF template if missing
ChipEffectFile.fromDataFile {aroma.affymetrix}Retrive an existing CEL file, or create from CDF template if missing
ChipEffectFile.getAM {aroma.affymetrix}Gets the log-intensities and log-ratios of chip effects for two arrays
ChipEffectFile.getCellIndices {aroma.affymetrix}Retrieves tree list of cell indices for a set of units
ChipEffectFile.getUnitGroupCellMap {aroma.affymetrix}Gets a (unit, group, cell) index map
ChipEffectFile.getXAM {aroma.affymetrix}Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
ChipEffectGroupMerge {aroma.affymetrix}The ChipEffectGroupMerge class
ChipEffectGroupMerge.process {aroma.affymetrix}Normalizes the data set
ChipEffectSet {aroma.affymetrix}The ChipEffectSet class
ChipEffectSet.extractExpressionSet {aroma.affymetrix}Extracts an in-memory ExpressionSet object
ChipEffectSet.getAM {aroma.affymetrix}Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file
ChipEffectSet.getBaseline {aroma.affymetrix}Gets the baseline signals across chromosomes
ChipEffectSet.getXAM {aroma.affymetrix}Gets the physical position, log-intensities and log-ratios of chip effects for two arrays
ChipEffectTransform {aroma.affymetrix}The ChipEffectTransform class
clearData.AffymetrixCelFile {aroma.affymetrix}Clears all or a subset of the fields in a CEL file