[BioC] gains and losses via mode shifting

Oscar Rueda omrueda at cnio.es
Tue Jul 1 11:45:46 CEST 2008

Dear Benjamin,

I'm not sure if I understand correctly your problem, but are your samples  
normalized to have the same median?

Oscar M. Rueda
Structural Computational Biology Group
Spanish National Cancer Centre (CNIO)
Madrid, SPAIN.

On Mon, 30 Jun 2008 13:02:46 +0200, Benjamin Otto  
<b.otto at uke.uni-hamburg.de> wrote:

> Hi,
> After the segmentation of CGH data in some papers the results are  
> frequently
> shifted by the density mode. To be more precise the mode of the highest  
> peak
> is used. However this procedure depends on the condition that there is
> clearly one prominent peak dominating the density function.
> Currently, in some of my samples, I do have the problem of two prominent
> peaks flanking the y-axis which make the decision about the correct shift
> direction a difficult one. Moreover in some of the cases a shift in one
> direction seems to be obvious, in some other cases a shift in the other
> direction seems more preferable and in a third group the preference is  
> not
> quite clear. But in all groups a segmentation profile in chromosomes 1-3  
> is
> nearly identical which suggests that I do observe the same gain or loss
> (depending on the shift direction) in all these samples.
> Does anyone have an idea how to assess this problem and how to solve it?  
> Is
> there another frequently used procedure aside the density mode shifting  
> used
> for such data?
> I do have pictures of some samples displaying the problem but they are  
> too
> big for the mailing list. Is there an official repository I can upload  
> them
> to?
> Thanks in advance, best regards,
> Benjamin
> ======================================
> Benjamin Otto
> University Hospital Hamburg-Eppendorf
> Institute For Clinical Chemistry
> Martinistr. 52
> D-20246 Hamburg
> Tel.: +49 40 42803 1908
> Fax.: +49 40 42803 4971
> ======================================

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