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| batchAdjust | Adjust microarray data for batch effects. |
| batchFilter | Remove differential features regarding array batches/lots. |
| diffAnalysis | Differential analysis. |
| loadGPR | A function to read raw data from gpr files. |
| mMsMatrix | Compute a reference minimum M statistic (n1 x n2)-matrix. |
| normalizeArrays | Normalize microarray data. |
| plotFeatures | Plot intensities of selected features. |
| plotFeaturesHeatmap | Plot feature intensities as a heatmap. |
| plotMAPlots | Check normalization results with MA plots. |
| plotNormMethods | Check normalization results with boxplots. |
| preselect | Score and preselect features. |
| printFeatures | Print biomarker candidate panel into a table. |
| pvaluePlot | Draw a p-value plot. |
| selectFeatures | Select features using frequency-based or ensemble feature selection. |
| shuffleData | Shuffles class labels to obtain random groups. |
| volcanoPlot | Draw a volcano plot. |