some have asked me about a reference for gcrma... a paper is now officially accpeted by the journal of the american statistical association (JASA). you can get the info here: http://www.bepress.com/jhubiostat/paper1/ there is a correspondace in Nature Biotechnology with a comparison to other methods as well: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d opt=Abstract&list_uids=15175677 -r ps - the latest updated version is quite different from the original.