Dear Biostar Community,
I've been struggling around, but there is no way I can find a paper describing the copy number variation detection method implemented by Agilent in its Workbench software, and called Aberration Detection Method - 2 (ADM-2).
I found some literature concerning the ADM-1 algorithm, but nothing on ADM-2. Is it copyrighted? But even so, shouldn't there be some white paper describing how it works compared to other segmentation methods (I found a Nature Methods paper comparing various CGH platforms, but even there the Authors just state that (not literal) Agilent CGH arrays are particularly good at detecting copy number aberrations with ADM-2, not going into detail on why that should be and not citing any reference for that algorithm.
Is there any free package implemented in R and BioConductor for implementing ADM-2 in CGH data?
Any information would be highly appreciated!