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Reference index for {aroma.affymetrix}

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

Function/ClassDescription
ParameterCelFile {aroma.affymetrix}The ParameterCelFile class
ParameterCelSet {aroma.affymetrix}The ParameterCelSet class
ParameterCelSet.extractDataFrame {aroma.affymetrix}Extract data as a data.frame for a set of arrays
ParameterCelSet.extractMatrix {aroma.affymetrix}Extract data as a matrix for a set of arrays
patch.AromaAffymetrix {aroma.affymetrix}Non-documented objects
pdInfo2Cdf {aroma.affymetrix}Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxillary CEL file for the same chip type
plotBoxplotStats.list {aroma.affymetrix}Plots a (merged or non-merged) list of boxplot.stats() elements
plotDensity.AffymetrixCelFile {aroma.affymetrix}Plots the density of the probe signals on the array
plotDensity.AffymetrixCelSet {aroma.affymetrix}Plots the densities of all samples
plotDensity.GenomeInformation {aroma.affymetrix}Plots the density of SNPs for a given chromosome
plotImage.AffymetrixCelFile {aroma.affymetrix}Displays a spatial plot of a CEL file
plotMvsA.AffymetrixCelFile {aroma.affymetrix}Plots log-ratio versus log-intensity in a scatter plot
plotMvsX.AffymetrixCelFile {aroma.affymetrix}Plots log-ratio versus another variable in a scatter plot
ProbeAffinityFile {aroma.affymetrix}The ProbeAffinityFile class
ProbeAffinityFile.getCellIndices {aroma.affymetrix}Retrieves tree list of cell indices for a set of units
ProbeLevelModel {aroma.affymetrix}The ProbeLevelModel class
ProbeLevelModel.findUnitsTodo {aroma.affymetrix}Identifies non-fitted units
ProbeLevelModel.fit {aroma.affymetrix}Estimates the model parameters
ProbeLevelModel.getChipEffectSet {aroma.affymetrix}Gets the set of chip effects for this model
ProbeLevelModel.getProbeAffinityFile {aroma.affymetrix}Gets the probe affinities for this model