Where Can I Find An Explanation For The Adm-2 Algorithm Used By Agilent For Array-Cgh Analysis?

Question

[zoppoli]

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!

Answer 1

[Ying W]

This is not the newest user guide but it is detailed here (pdf on page 451). If you have a license for their software, you could probably email their customer service and ask for the most recent user guide. If its developed by the company, they probably own the intellectual property rights on it. There is probably not an exact implementation in BioConductor but there are several packages that will process CGH data.

Answer 2

[Henrik Bengtsson]

Updated link to the 'Agilent Genomic Workbench 7.0 (Agilent Technologies)' manual:

http://www.chem.agilent.com/library/usermanuals/public/g3800-90042_cgh_interactive.pdf

The ADM-1 and ADM-2 methods are briefly described in Section 'Statistical Algorithms' (pp 493-497).