[BioC] gains and losses via mode shifting

[J.Oosting at lumc.nl]

> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of Benjamin Otto
> Sent: maandag 30 juni 2008 14:09
> I was hoping there would be a solution, which incorporates some global
> information about all samples. Suppose I would only have one samples
with
> not so obvious shifting but a segmentation following all others
clearly,
> then I could use this information for the correction. Unfortunately
it's
> not so easy in my case. Yet it naturally makes a difference if my
samples
> group 50 percent to 50 percent according to gain and loss calls versus
> when they agree on one of the solutions.
> 
> How do I know in that case from a pure bioinformatical point of view
that
> my processing procedures provide reliable results and not some sort of
> gambling result?
> 
> Benjamin

We perform flowcytometry to determine ploidy in a lot of cases to make
sure we don't miss events like tetraploidization, which can be
impossible to pick up with arrayCGH when there are no extra deletion
events in the tissue.

Jan Oosting