Hi All, I have a question about analyzing aCGH data with huge number of probes on a single chromosome. We have a set of customized NimbleGen aCGH human sample data. Each sample has 40 million probes. Even a single chromosome has >3M probes. I tried some R-based and Matlab-based aCGH analysis software to analyze just a single chromosome in a single sample using our supercomputer, but no hopes! Some software just show error messages (works fine for small data sets) and some software can not complete the analysis even after 1-2 days CPU time. I am wondering whether any people in the list have experience in analyzing the aCGH data with such a scale. If you have, can you share some your experience with me? Will it be a good idea to first divide the chromosome into some small pieces (say each pieice has 10,000 probes) and then run the algorithm on each piece of the chromosome? Thanks you! 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

On Fri, Apr 4, 2008 at 11:38 AM, pingzhao Hu <phu at="" sickkids.ca=""> wrote: > > Hi All, > I have a question about analyzing aCGH data with huge number of > probes on a single chromosome. > We have a set of customized NimbleGen aCGH human sample data. Each sample > has 40 million probes. Even a single chromosome has >3M probes. > > I tried some R-based and Matlab-based aCGH analysis software to > analyze just a single chromosome in > a single sample using our supercomputer, but no hopes! Some software > just show error messages (works fine for small > data sets) and some software can not complete the analysis even after > 1-2 days CPU time. > > I am wondering whether any people in the list have experience in > analyzing the aCGH data with such a scale. > If you have, can you share some your experience with me? > > Will it be a good idea to first divide the chromosome into some small > pieces (say each pieice has 10,000 probes) and then run the algorithm > on each piece of the chromosome? What are the goals of the analysis? What types of samples (cancer, comparative genomics, normal DNA)? And what methods have you tried? Sean