[BioC] Calling genes present or absent in CGH data

[John Zhang]

You may want to try the segment function of DNAcopy to identify regions with 
gains or losses. If you then would like to identify regions whowing gains/losses 
across samples, look at packages like CNTools, cghMCR, CGHcall, and CGHregions.

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>Subject: [BioC] Calling genes present or absent in CGH data
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>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?
>
>thanks for any advice
>
>Adam
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084