I wish to reduce a 243440-line array CGH data set, in a single GEO file (GSE20574), from an Agilent 244A aCGH array. My primary goal is to identify deleted, normal, and gain/amplification regions on all chromosomes, and then to identify genes annotated to these regions which may have been affected. Never having done an analysis like this before, I'd be grateful for advice. Looking at the bioc package repository, I see a number of CGH-related packages, but I am not quite sure which to use. What do I read? Where do I start? Thanks. - Paul