Hi Allen, You can also try PLASQ package http://genome.dfci.harvard.edu/~tlaframb/PLASQ/, which do normalization and CNV inference using affy 500k data. pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital for Sick Children Research Institute MaRS Centre - East Tower 101 College Street, Room 15-705 Toronto, Ontario, M5G 1L7, Canada Tel.: (416) 813-7654 x6016 Email: phu at sickkids.ca Web: http://www.tcag.ca/statisticalAnalysis.html