Man pages for puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

bcombCombining replicates for each condition
calcAUCCalculate Area Under Curve (AUC) for a standard ROC plot.
calculateFCCalculate differential expression between conditions using FC
calculateLimmaCalculate differential expression between conditions using...
calculateTtestCalculate differential expression between conditions using...
clusterApplyLBDotsclusterApplyLB with dots to indicate progress
clusterNormEZero-centered normalisation
clusterNormVarAdjusting expression variance for zero-centered normalisation
Clust.exampleEThe example data of the mean gene expression levels
Clust.exampleStdThe example data of the standard deviation for gene...
Clustii.exampleEThe example data of the mean gene expression levels
Clustii.exampleStdThe example data of the standard deviation for gene...
compareLimmapumaDECompare pumaDE with a default Limma model
createContrastMatrixAutomatically create a contrast matrix from an ExpressionSet...
createDesignMatrixAutomatically create a design matrix from an ExpressionSet
create_eset_rCreate an ExpressionSet from a PPLR matrix
DEResult-classClass DEResult
erfcThe complementary error function
eset_mmgmosAn example ExpressionSet created from the Dilution data with...
exampleEThe example data of the mean gene expression levels
exampleStdThe example data of the standard deviation for gene...
exprReslt-classClass exprReslt
gmhtaCompute gene and transcript expression values and standard...
gmoExonCompute gene and transcript expression values and standard...
hcombCombining replicates for each condition with the true gene...
hgu95aphisEstimated parameters of the distribution of phi
igmoExonSeparately Compute gene and transcript expression values and...
justmgMOSCompute mgmos Directly from CEL Files
justmmgMOSCompute mmgmos Directly from CEL Files
legend2A legend which allows longer lines
license.pumaPrint puma license
matrixDistanceCalculate distance between two matrices
mgmosmodified gamma Model for Oligonucleotide Signal
mmgmosMulti-chip modified gamma Model for Oligonucleotide Signal
normalisation.gsGlobal scaling normalisation
numFPNumber of False Positives for a given proportion of True...
numOfFactorsToUseDetermine number of factors to use from an ExpressionSet
numTPNumber of True Positives for a given proportion of False...
orig_pplrProbability of positive log-ratio
plotErrorBarsPlot mean expression levels and error bars for one or more...
plotHistTwoClassesStacked histogram plot of two different classes
plot-methodsPlot method for pumaPCARes objects
plotROCReceiver Operator Characteristic (ROC) plot
plotWhiskersStandard errors whiskers plot
PMmmgmosMulti-chip modified gamma Model for Oligonucleotide Signal...
pplrProbability of positive log-ratio
pplrUnsortedReturn an unsorted matrix of PPLR values
pumaclustPropagate probe-level uncertainty in model-based clustering...
pumaClustiiPropagate probe-level uncertainty in robust t mixture...
pumaCombCombining replicates for each condition
pumaCombImprovedCombining replicates for each condition with the true gene...
pumaDECalculate differential expression between conditions
pumaDEUnsortedReturn an unsorted matrix of PPLR values
pumaFullPerform a full PUMA analysis
pumaNormalizeNormalize an ExpressionSet
puma-packagepuma - Propagating Uncertainty in Microarray Analysis
pumaPCAPUMA Principal Components Analysis
pumaPCAExpectations-classClass pumaPCAExpectations
pumaPCAModel-classClass pumaPCAModel
pumaPCARes-classClass pumaPCARes
removeUninformativeFactorsRemove uninformative factors from the phenotype data of an...
puma documentation built on Nov. 1, 2018, 4:28 a.m.