[BioC] copy number for Affy 6.0

Henrik Bengtsson hb at stat.berkeley.edu
Wed Aug 6 04:50:33 CEST 2008

Have a look at aroma.affymetrix


There is a vignette illustrating how you can get raw copy-number
estimates on GenomeWideSNP_6 (GWS6) (and all other Affymetrix SNP/CN

The CNAT method/algorithm does not apply to the GWS5/6 chip types -
only 500K and before.

For Affymetrix solutions, have a look at Affymetrix Power Tools (APT),
which is an open-source cross-platform command line based set of
methods.  FYI, the Affymetrix Genotype Console (GTC) analyzes GWS6 and
is a Windows GUI that utilizes APT for its processing (according to
the docs of the latest release; it is no longer relying on Matlab



On Tue, Aug 5, 2008 at 7:29 PM, Rob Scharpf <rscharpf at jhsph.edu> wrote:
> Hi,
> For the Affy 6.0 platform, I would like to know the default tool for
> obtaining copy number estimates prior to smoothing across loci (raw copy
> number).  If CNAT is the default, is there a command-line version of this
> tool available, or an implementation of a CNAT-equivalent in R?
> Thanks,
> Rob
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