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 [[alternative HTML version deleted]]