ECDFPlot                Plot empirical cumulative distribution function
                        for correlations.
PCAPlot                 Plot principle component analysis for gene
                        expression data.
RLEPlot                 Plots different versions of relative log
                        expression plots
RUVNaiveRidge           Removal of unwanted variation for gene
                        correlations.
RUVcorr                 Removal of unwanted variation for gene-gene
                        correlations.
assessQuality           Quality assessment for cleaning procedures.
background              Randomly choose background genes.
calculateThreshold      Calculates the correlation threshold.
compareRanks            Compare ranking of known reference gene pairs.
correlationPlot         Correlation plot to compare estimated
                        correlations with true correlations.
eigenvaluePlot          Plot eigenvalues of SVD of the negtaive
                        controls.
empNegativeControls     Empirically choose negative control genes.
findWeights             Finds weights of each level of a factor.
genePlot                Plot of means and inter-quantile ranges of all
                        genes.
histogramPlot           Plot histogram of correlations.
is.Threshold            Checking 'Threshold' class.
is.Weights              Checking 'Weights' class.
is.optimizeParameters   Checking 'optimizeParameters' class.
is.simulateGEdata       Checking 'simulateGEdata' class.
optimizeParameters      Optimize parameters of removal of unwanted
                        variation.
plot.optimizeParameters
                        Plots an object of class 'optimizeParameters'.
plotDesign              Plot nested design structure.
plotThreshold           Plots an object of class 'Threshold'.
print.simulateGEdata    Print an object of class 'simualteGEdata'.
prioritise              Prioritising candidate genes.
simulateGEdata          Simulate gene expression data.
wcor                    Calculate weighted correlations.
