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

[Sean Davis]

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