Hi, I am trying to replicate the results gained from the Affymetrix SNP 10K experiments in the cancer genome project (http://www.sanger.ac.uk/genetics/CGP/). The publicly accessible data files (ftp://ftp.sanger.ac.uk/pub/CGP/affy/) are found in this format: SNP_NUMBER SNP_NAME PMS MMS PMA MMA 1 SNP_A-1513509 5901.9 3925.3 3815.1 2648.4 2 SNP_A-1513556 6280.3 5403.5 7412.3 5743.5 3 SNP_A-1518411 7047.3 3734.9 4357.4 2315.6 where according to the README: SNP_NUMBER = Affymetrix internally assigned reference number SNP_NAME = Affymertix SNP identifier PMS = Perfect match (sense) intensity value MMS = Mismatch (sense) intensity value PMA = Perfect match (antisense) intensity value MMA = Mismatch (antisense) intensity value Does anyone have any idea on how I can get the copy number from this data? Tried all the possible ratios but they do not seem to produce accurate results. Daniel Brewer -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 Fax: +44 (0) 20 8722 4141 Email: daniel.brewer at icr.ac.uk