Hi, I am new to bioconductor. Is there a good package/work flow that does copy 
number/LOH analysis for Affy 100K chips, starting from CEL files? I have 100K 
data from ~ 30 tumor samples; and I plan to download 100K trios data (90 healthy 
individuals) as normal references from Affymetrix website. Do I really need 
normal references for copy number/LOH analysis? Cheng Li of dChip had a paper in 
PLoS Computational Biology 2006 describing that dChip can infer LOH from 
unpaired tumor samples without using normal references, is there a package in 
bioconductor that can do this?

Thank you.

John



      
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