Hello I have a questions about correlation of outcomes from Rosetta and Limma. I have done Agilent direct hyb's (one condition versus another). In Rosetta I have splitted ratios without common references and than have done two sample Ttest. In Limma I also splitted channels and than fitted linear model. I have posted design in previous BioC thread with subj "Design question in LIMMA". The outcome of the Toptable is different (from 120 signatures only 20 intersects). Does anybody experienced that problem or have expertise of statistical treatment of twocolors direct ratio based arrays in Rosetta and Limma simultaneously. Regards, Nataliya -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064