| batchAdjust | Adjust microarray data for batch effects. | 
| batchFilter | Remove differential features regarding array batches/lots. | 
| batchFilter.anova | Remove features which are differential regarding microarray batches / lots in a multi-batch scenario. | 
| diffAnalysis | Differential analysis. | 
| loadGPR | Importing raw data from gpr files. | 
| mMsMatrix | Compute a reference minimum M statistic (n1 x n2)-matrix. | 
| normalizeArrays | Normalize microarray data. | 
| plotArray | Plot ProtoArray expression intensities in the original arrangement mimicking the original scan image. | 
| plotFeatures | Plot intensities of features. | 
| plotFeaturesHeatmap | Plot feature intensities as a heatmap. | 
| plotFeaturesHeatmap.2 | Alternative function to 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 features 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. |