[BioC] Call for comments on analyzing aCGH data with huge number of probes on a single chromosome

[pingzhao Hu]

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