[BioC] snapCGH question

[Ramon Diaz-Uriarte]

On Wednesday 18 April 2007 12:34, Sean Davis wrote:
> On Wednesday 18 April 2007 06:25, Federico Abascal wrote:
> > Hello,
> >
> > I am learning about the snapCGH package, and would like to understand
> > something:
> > Is it required to have the information about position of the clone in
> > the array (row and column number) in order to use the snapCGH package? I
> > guess the bioHMM take this into account, but I am not sure. The aCGH
> > package does not require this kind of information.
>
> Just Chr and Position are needed, I believe.
>

If you use the BioHMM method, you will want to take into account the position. 
aCGH (which uses a homogeneous HMM where distances between spots are assumed 
identical) does not require that you use any meaningful distance (only the 
order).

Note that snapCGH includes wrappers for the HMM method in aCGH.



> > In addition, I will be pleased to know the opinion of some experienced
> > user, to determine if bioHMM does work better than aCGH in practice.
> > (in the bioHMM application note no comparison is done)
>
> You may want to look at this paper:
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=A
>bstractPlus&list_uids=16159913
>
> It doesn't answer your question directly.  However, it may help your to
> reframe the question slightly.
>

We have done some further comparisons, which include BioHMM, HMM, CBS and 
<start advertisment> our own non-homogeneous HMM </end advertisment>, using 
the same data as in Willenbrock and Fridlyand, but additionally 
adding "holes" or gaps, which is where you'd expect non-homogeneous HMMs to 
show a clear advantage over homogeneous HMMs that assume equally spaced 
genes.

You can access it from

http://biostats.bepress.com/cobra/ps/art9/


Hope that helps.

Best,

R.



> Sean
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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
(http://ligarto.org/rdiaz/0xE89B3462.asc)



**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en s...{{dropped}}