[BioC] Calling genes present or absent in CGH data

Sean Davis seandavi at gmail.com
Fri Jan 22 14:50:53 CET 2010

On Fri, Jan 22, 2010 at 8:28 AM, adam_pgsql <adam_pgsql at witneyweb.org> wrote:
> Hi,
> I have a CGH data set (two colour spotted array data) where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent?

Hi, Adam.

CGH data are generally treated somewhat differently than gene
expression and so a different set of tools is often used.  You might
look at any of a dozen or so methods related to CGH segmentation.
There is a literature comparing various methods, also.  For starters,
you might look here:


For literature, consider checking out this as a "review":


And for an interesting approach to comparison between methods, see:



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