Hello, I'd like to make clear how the 'Heat Map for Genes in Dataset' which is one of plots in the '(project name).global.plots.pdf' and is generated by the Gene Set Enrichment Analysis R code (GSEA.1.0.R)? The code is available as R-GSEA at: <http: www.broadinstitute.org="" cancer="" software="" gsea="" wiki="" index.php="" r-g="" sea_readme=""> <http: www.broadinstitute.org="" gsea="" downloads.jsp=""> My understanding is that each row represents one gene in the data set which is somehow normalized and the columns are grouped according to the lables provided by the person running the code. My question is how the rows in the heat map are sorted since I have tried several different clustering methods with my data and I've never gotten such impressive picture as with this code. The heat map itself is generated by the function 'GSEA.HeatMapPlot()' which is defined by the script but I find it difficult to decipher how the rows are sorted although complete R code is provided. Anyone can help please? Regards, Radek Radek Blatny, MSc. Institute of Molecular Genetics Department of Mouse Molecular Genetics (Jiri Forejt unit) Czech Academy of Sciences Videnska 1083 142 20, Prague Czech Republic Tel. (+420) 241 062 260 Fax (+420) 241 062 154 http://www.img.cas.cz/mmg email: blatny at img.cas.cz Skype name: blatny