[BioC] gains and losses via mode shifting

Benjamin Otto b.otto at uke.uni-hamburg.de
Mon Jun 30 13:02:46 CEST 2008


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

Thanks in advance, best regards,


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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