| Function | Description |
| bg.correct.LESN | LESN - Low End Signal is Noise Background corrections |
| fitPLM | Fit a Probe Level Model to Affymetrix Genechip Data. |
| MAplot | Relative M vs. A plots |
| normalize.AffyBatch.quantiles.probeset | Quantile Normalization applied to probesets |
| normalize.exprSet.quantiles | Normalization applied to exprSets |
| normalize.scaling | Scaling normalization |
| PLMset2exprSet | Convert a PLMset to an exprSet |
| PLMset-class | Class PLMset |
| pseudoColorBar | Coloring pseudo chip images |
| rmaPLM | Fit a RMA to Affymetrix Genechip Data as a PLMset |
| threestep | Three Step expression measures |
| threestepPLM | Three Step expression measures returned as a PLMset |