I'm currently working on aCGH data of Triple Negative Breast Cancer patients xenografts and primary tumor samples. A substantial amount of my samples is highly aberrated which leads to offsets of the diploid bands away from the log2ratio of 0.
I found an article on a prospective normalization for this: http://www.biomedcentral.com/1471-2164/8/382/ which includes the popLowess package in R: http://baseplugins.thep.lu.se/wiki/se.lu.onk.popLowess
However this a method from 2007 and I was wondering whether other approaches now exist that perhaps perform better (or different) aCGH normalizations. Ideas are very much welcome, thanks.
Sjors van Heuveln