[BioC] snapCGH and CGH method evaluation
sdavis2 at mail.nih.gov
Mon Dec 4 14:33:00 CET 2006
João Fadista wrote:
> Dear all,
> snapCGH -> Does anyone know how to display regions of gain or loss across multiple samples in the same plot? I am asking this with the purpose of finding common breakpoints and regions of common gain or loss between samples.
The "standard" way of doing this is a "frequency plot". Simply sum
across samples all the probes that are greater (less) than a certain
threshold and plot them along the chromosome. I don't personally like
them very much, but it is easy to produce. Also, you might look at the
package cghMCR and also at the java executable called STAC.
> CGH method evaluation -> Does anyone knows if there is any CGH package that estimate the statistical significance of the detected copy number changes and then rank them accordingly?
This is a very challenging problem. You, as the researcher, will
probably need to decide what you think is important (short segments,
long segments, high-copy number gains, homozygous deletions, copy number
polymorphisms, etc.) and design your own methods for pulling these out.
A simple statistical test does not do the trick, in my experience, for
pulling out all the relevant information. If you really want something
that gives statistical significance, you might want to look at an
article by Lipson et al., in RECOMB 2005 (don't have the exact reference
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