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

[pingzhao Hu]

Sean,
Thanks!
The gold is to identify copy number variation from normal human samples.
I have tried CBS, cghFLasso 
(http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxm013v1)
our own method 
(http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxl035v1), 
etc methods.

Pingzhao


At 11:45 AM 4/4/2008, Sean Davis wrote:
>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



========================================
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