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Reference index for {aroma.affymetrix}

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

Function/ClassDescription
AffymetrixCelFile.plotMvsA {aroma.affymetrix}Plots log-ratio versus log-intensity in a scatter plot
AffymetrixCelFile.plotMvsX {aroma.affymetrix}Plots log-ratio versus another variable in a scatter plot
AffymetrixCelFile.readRawData {aroma.affymetrix}Gets all or a subset of the fields in a CEL file
AffymetrixCelFile.readUnits {aroma.affymetrix}Reads CEL data unit by unit
AffymetrixCelFile.setCdf {aroma.affymetrix}Sets the CDF structure for this CEL file
AffymetrixCelFile.smoothScatterMvsA {aroma.affymetrix}Plots log-ratio versus log-intensity in a smooth scatter plot
AffymetrixCelFile.updateUnits {aroma.affymetrix}Updates CEL data unit by unit
AffymetrixCelFile.writeImage {aroma.affymetrix}Writes a spatial image of the signals in the CEL file
AffymetrixCelSet {aroma.affymetrix}The AffymetrixCelSet class
AffymetrixCelSet.bgAdjustGcrma {aroma.affymetrix}Applies probe sequence based background correction to a set of CEL files
AffymetrixCelSet.bgAdjustOptical {aroma.affymetrix}Applies optical background correction to a set of CEL files
AffymetrixCelSet.bgAdjustRma {aroma.affymetrix}Applies RMA background correction to a set of CEL files
AffymetrixCelSet.calculateParametersGsb {aroma.affymetrix}Computes parameters for adjustment of specific binding
AffymetrixCelSet.doFIRMA {aroma.affymetrix}Finding Isoforms using Robust Multichip Analysis (FIRMA)
AffymetrixCelSet.extractAffyBatch {aroma.affymetrix}Extracts an in-memory AffyBatch object from the CEL set
AffymetrixCelSet.extractFeatureSet {aroma.affymetrix}Extracts CEL signals an in-memory FeatureSet object
AffymetrixCelSet.extractMatrix {aroma.affymetrix}Extract data as a matrix for a set of arrays
AffymetrixCelSet.getAverageFile {aroma.affymetrix}Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set
AffymetrixCelSet.getCdf {aroma.affymetrix}Gets the CDF structure for this CEL set
AffymetrixCelSet.getChipType {aroma.affymetrix}Gets the chip type for this CEL set