Visualization of Large Microarray Experiments with Space Maps
Heatmaps and profile plots are effective techniques to visualize expression profiles of several hundred genes across a few dozen samples. However, these techniques do not scale to data sets with expression profiles that have been measured across several hundred samples or even thousands of samples. Our motivation to find a solution to this scaling problem is based on the observation that with increasingly mature and affordable microarray platforms, the number of studies in ArrayExpress  including hundreds of samples has been increasing steadily over the years.
N Gehlenborg and A Brazma. “Visualization of Large Microarray Experiments with Space Maps” BMC Bioinformatics 10(Suppl 13):O7 (2009).