[BioC] Calling genes present or absent in CGH data

John Zhang jzhang at jimmy.harvard.edu
Fri Jan 22 14:42:03 CET 2010

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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>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
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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