[BioC] Calling genes present or absent in CGH data

[Sean Davis]

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:

http://bioconductor.org/packages/release/CopyNumberVariants.html

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

http://www.ncbi.nlm.nih.gov/pubmed/16081473

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

http://www.ncbi.nlm.nih.gov/pubmed/18296463

Sean