3 packages on Bioconductor
Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.
Graphically displays correlation in microarray data that is due to insufficient normalization
This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).