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 > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] --- Robin Andersson, PhD student Linnaeus Centre for Bioinformatics Uppsala University BMC, Box 598, SE-751 24 Uppsala, Sweden phone: +46 18 471 66 86 (admin: 66 90) fax: +46 18 471 66 98 office: BMC, C6:315a email: [EMAIL PROTECTED] http://www.lcb.uu.se/~robina/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
