DNAcopy package in R

Hi All:

Has anyone analyzed Illumina 550K data using DNAcopy package? I have around
2300 samples. According to
Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single
sample for Affymetrix 100K. I am afraid it will take too long to analyzed my
data. Anybody has an idea? Thanks!

Best,

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