Thank you Simon and Gordon for your replies. The models are now converging with increased iterations in DESeq. Gordon, thank you for pointing me towards the difference in the EdgeR GLM compared with that of DESeq. We will also try running the models in EdgeR and see how the results differ from those of DESeq. Cheers, Seanna -- Seanna McTaggart Centre for Immunity, Infection and Evolution School of Biological Sciences Ashworth Laboratories University of Edinburgh Edinburgh EH9 3JT Scotland, UK Tel +44 131 650 8682 Fax +44 131 650 6564 E-mail: smctagga at staffmail.ed.ac.uk <http: www.biology.ed.ac.uk="" research="" groups="" tlittle="" people.html=""> <http: ciie.bio.ed.ac.uk="" centre=""> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.