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| 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. |