| aveProbe | Transform Affymetrix data so that unique genes with multiple probes are represented by a single expression value on each array. |
| corplot | Produce a plot for jointly visualizing pooled correlation information and expression data for selected genes |
| corplot2 | Produce a plot for jointly visualizing unpooled correlation information and expression data for selected genes |
| getImat | Generate an indicator matrix |
| pcot2 | Principal Coordinates and Hotelling's T-Square |