Hi Jari,
Thanks for your comments.
On Jan 26, 2008, at 12:43 AM, Jari Häkkinen wrote:
Nice work. I've successfully tested the apt-summarize plug-in. I do
not
have any genotype data so I have to leave that for someone else to
test.
I miss a short description of the two plug-ins. How to use them and
what
to expect from them.
I have added a README file to the package.
Specifically the genotyoe plug-in requires some
additional files (or one file). Is the chrx file alwasy the same for a
given .cdf (array design in BASE speak)?
No, it is not the same for different chips. The files may be
downloaded from www.affymetrix.com.
The chrx files are not required, if they are not passed to the APT
Genotype plugin the analysis will be performed without the information
about these SNPs (by sending the --chrX-force flag to apt-probeset-
genotype).
If yes, maybe we should extend
array design to also store the chrx file for seamless use. Also,
should
there be more than one Affy raw data type, one for expression and
another for snp?
This would be really nice. Then it would be possible to implement
plugins that are specific to a certain chip or a group of chips
(subgroup of the affymetrix data type).
Jim Collet made an inquiry about support for 'apt-cel-extract' to the
mailing list in the beginning of this year. How do we proceed to get
this algorithm (and others) into the APT plug-in set?
I am not sure. Perhaps some functions in the abstract class APTPlugin
need to be rewritten to make it work. I identified the common parts of
the APT Genotype and Summarize plugins and put these into the abstract
class. The choices made may not be the best for 'apt-cel-extract'.
Cheers,
Robin
Cheers,
Jari
Robin Andersson skrev:
Hi all,
A plugin package for execution of the Affymetrix Power Tools
apt-probeset-summarize and apt-probeset-geneotype are available for
download from:
http://madr.lcb.uu.se/browser/plugins/se/uu/lcb/APT/tags/0.2
From this repository you can download a precompiled jar file or the
source code. See the INSTALL file for instructions. This package is a
suggested replacement of the affymetrix package including the Plier
and
RMAExpress plugins.
Robin
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Robin Andersson, PhD student
Linnaeus Centre for Bioinformatics
Uppsala University
BMC, Box 598, SE-751 24 Uppsala, Sweden
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