[BioC] gains and losses via mode shifting

Benjamin Otto b.otto at uke.uni-hamburg.de
Tue Jul 1 12:54:59 CEST 2008

The logratios are loess normalized with limma and the smoothing/segmentation
is done with DNAcopy.

The problem is that some of the samples seem to belong to maniac tumors. The
intriguing point for some samples is not really chromosomes 1-3, I only use
them as a kind of clue, but more that I do observe two possible base lines
which exhibit nearly comparable peaks in my density function. Each of them
look as if it could be the real zero line, but I don't know which one. If I
used some criterion like 2*SD(50% quantile) for detection of gains or losses
then the shift direction would make a difference.


-----Ursprüngliche Nachricht-----
Von: Oscar Rueda [mailto:omrueda at cnio.es] 
Gesendet: Tuesday, July 01, 2008 11:46 AM
An: Benjamin Otto; bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] gains and losses via mode shifting

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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