[BioC] gains and losses via mode shifting

[Sean Davis]

On Mon, Jun 30, 2008 at 7:54 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Mon, Jun 30, 2008 at 7:02 AM, 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?
>
> We use the lower of the two modes when there is a "tie".

By lower, I mean leftmost on the x-axis of the density plot.

> Since CGH
> data is naturally censored at the low end, this makes some sense,
> biologically, to do.  However, this is not a perfect solution nor can
> there usually be one, as heterogeneity appears to be almost
> universally present.  So, there is little chance of determining the
> absolute copy number which translates to an inability to absolutely
> determine the correct mode.
>
> Sean
>