Which free software for the analysis of Affymetrix aCGH/SNP array data can you recommend

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Santhi Rekha

https://sites.google.com/site/dchipsoft/home

http://www.bcm.edu/garp/index.cfm?PMID=3113

these links contain some software's that may useful for you.

http://www.openbioinformatics.org/penncnv/ check this link also...

Jan Pawel Jastrzebski

Obviously R-project and bioconductor, there is no better!