Dear Made4 users, There was a bug in heatplot in made4 v1.10. The default color scheme of the heatmap had the colors "reversed". As this is potentially confusing to users, I have corrected this bug in Bioconductor and the version number is incremented to 1.10.1 Now down-regulated genes are blue (cold color) and up-regulated genes are red/brown (warm colors). heatplot() does "Eisen" hierarchical cluster analysis, in that it uses 1-Pearson Correlation as the default distance and average linkage as the default joining method. I had implmented a new color scheme in version 1.10. The previous Version 1.9 used a red-green color scheme, but in v1.10 heatplot uses the color scheme of red/brown - blue as defined in Colors defined by Huber, Li & Gentleman, Chapter 10, Bioinformatics & Computational Biology Solutions using R & Bioconductor (2006). You can of course, still use the old scheme, by setting cols.default=FALSE. Regards Aedin