[BioC] segmentation aCGH data

[Ramon Diaz-Uriarte]

Dear John,

On Wednesday 10 October 2007 15:52, jhs1jjm at leeds.ac.uk wrote:
> Hi list,
>
> I've been looking at 3*44k and 2*244k agilent CGH arrays. To date I've
> used limma to read in the processed signals (no background correction
> or normalization as this has been done), then the DNAcopy package for
> segmentation as well as the snapCGH package to employ other
> segmentation methods rather than use each segmentation package
> individually.
>
> Firstly using the DNAcopy segmentation I can see a significant pattern
> across my 3*44k arrays which disappears when I perform the step to
> remove unnecessary change points due to trends in the data. As these

How exactly are you removing "unnecesary change points due to trends in the 
data"?


> are in the same locations across the 3 arrays then is it likely that
> this is biologically significant rather than being a trend? Obviously
> others do not have a definitive answer for this but I wondered if
> anyone had seen similar results in a different scenario.
>
> Additionally I'm wondering what segmentation methods people have tended
> to employ. The heterogeneous nature of my data means that I need to
> identify  single probe as well as larger region aberrations and I'd
> read that the CBS algorithm is not particular suited to doing this?

If you run the "smooth.CNA" function (in the DNAcopy package), as it is 
recommended in the documentation for DNAcopy (IIRC), then single probe 
aberrations are not detectable (you are smoothing them away).

Single probe aberrations might be detected with the HMM model in snapCGH or 
our HMM model in RJaCGH, available from CRAN 
(http://cran.r-project.org/src/contrib/Descriptions/RJaCGH.html). (Details of 
the method available from the paper: 
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030122). 


Best,

R.


> Apologies   if this is a bit vague.
>
> Thanks for any input,
>
> John
>
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-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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