| 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. | 
| ECDFPlot | Plot empirical cumulative distribution function for correlations. | 
| eigenvaluePlot | Plot eigenvalues of SVD of the negtaive controls. | 
| empNegativeControls | Empirically choose negative control genes. | 
| empNegativeControls.default | Empirically choose negative control genes. | 
| empNegativeControls.simulateGEdata | 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.optimizeParameters | Checking 'optimizeParameters' class. | 
| is.simulateGEdata | Checking 'simulateGEdata' class. | 
| is.Threshold | Checking 'Threshold' class. | 
| is.Weights | Checking 'Weights' class. | 
| optimizeParameters | Optimize parameters of removal of unwanted variation. | 
| PCAPlot | Plot principle component analysis for gene expression data. | 
| 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. | 
| RLEPlot | Plots different versions of relative log expression plots | 
| RUVcorr | Removal of unwanted variation for gene-gene correlations. | 
| RUVNaiveRidge | Removal of unwanted variation for gene correlations. | 
| RUVNaiveRidge.default | Removal of unwanted variation for gene correlations. | 
| RUVNaiveRidge.simulateGEdata | Removal of unwanted variation for gene correlations. | 
| simulateGEdata | Simulate gene expression data. | 
| wcor | Calculate weighted correlations. |