Clust.exampleE          The example data of the mean gene expression
                        levels
Clust.exampleStd        The example data of the standard deviation for
                        gene expression levels
Clustii.exampleE        The example data of the mean gene expression
                        levels
Clustii.exampleStd      The example data of the standard deviation for
                        gene expression levels
DEResult                Class DEResult
bcomb                   Combining replicates for each condition
calcAUC                 Calculate Area Under Curve (AUC) for a standard
                        ROC plot.
calculateFC             Calculate differential expression between
                        conditions using FC
calculateLimma          Calculate differential expression between
                        conditions using limma
calculateTtest          Calculate differential expression between
                        conditions using T-test
clusterApplyLBDots      clusterApplyLB with dots to indicate progress
clusterNormE            Zero-centered normalisation
clusterNormVar          Adjusting expression variance for zero-centered
                        normalisation
compareLimmapumaDE      Compare pumaDE with a default Limma model
createContrastMatrix    Automatically create a contrast matrix from an
                        ExpressionSet and
createDesignMatrix      Automatically create a design matrix from an
                        ExpressionSet
create_eset_r           Create an ExpressionSet from a PPLR matrix
erfc                    The complementary error function
eset_mmgmos             An example ExpressionSet created from the
                        Dilution data with mmgmos
exampleE                The example data of the mean gene expression
                        levels
exampleStd              The example data of the standard deviation for
                        gene expression levels
exprReslt-class         Class exprReslt
hcomb                   Combining replicates for each condition with
                        the true gene expression
hgu95aphis              Estimated parameters of the distribution of phi
justmgMOS               Compute mgmos Directly from CEL Files
justmmgMOS              Compute mmgmos Directly from CEL Files
legend2                 A legend which allows longer lines
license.puma            Print puma license
matrixDistance          Calculate distance between two matrices
mgmos                   modified gamma Model for Oligonucleotide Signal
mmgmos                  Multi-chip modified gamma Model for
                        Oligonucleotide Signal
normalisation.gs        Global scaling normalisation
numFP                   Number of False Positives for a given
                        proportion of True Positives.
numOfFactorsToUse       Determine number of factors to use from an
                        ExpressionSet
numTP                   Number of True Positives for a given proportion
                        of False Positives.
orig_pplr               Probability of positive log-ratio
plot-methods            Plot method for pumaPCARes objects
plotErrorBars           Plot mean expression levels and error bars for
                        one or more probesets
plotHistTwoClasses      Stacked histogram plot of two different classes
plotROC                 Receiver Operator Characteristic (ROC) plot
plotWhiskers            Standard errors whiskers plot
pplr                    Probability of positive log-ratio
pplrUnsorted            Return an unsorted matrix of PPLR values
puma-package            puma - Propagating Uncertainty in Microarray
                        Analysis
pumaClust               Propagate probe-level uncertainty in
                        model-based clustering on gene
pumaClustii             Propagate probe-level uncertainty in robust t
                        mixture clustering on
pumaComb                Combining replicates for each condition
pumaCombImproved        Combining replicates for each condition with
                        the true gene expression
pumaDE                  Calculate differential expression between
                        conditions
pumaDEUnsorted          Return an unsorted matrix of PPLR values
pumaFull                Perform a full PUMA analysis
pumaNormalize           Normalize an ExpressionSet
pumaPCA                 PUMA Principal Components Analysis
pumaPCAExpectations-class
                        Class pumaPCAExpectations
pumaPCAModel-class      Class pumaPCAModel
pumaPCARes-class        Class pumaPCARes
removeUninformativeFactors
                        Remove uninformative factors from the phenotype
                        data of an
