Hi Markus, Thanks for your comments. For some reason I missed the 1.8.5 release of Affymetrix Power Tools. We have only run it on version 1.8.0. I have added a ticket for the requested improvements to our trac: http://madr.lcb.uu.se/ticket/128 .
Users of se.uu.lcb.APT version 0.2 should use Affymetrix Power Tools version 1.8.0. The next release would support the latest release. Regarding point 2, I see that version 1.8.5 of Affymetrix Power Tools now passes error messages to stderr rather than to stdout. This was not the case in previous versions. Hence, it was difficult to catch error messages before. Cheers, Robin On Feb 7, 2008, at 6:17 PM, Markus Ringnér wrote: > Hi Robin and everyone, > > Thanks for the APT plugin it works nicely. I have played around with > the > apt-probeset-genotype part and have some feedback. > > 1) The --chrX-force flag does not seem to be available in apt-1.8.5 > anymore, so the plugin crashes when it is run without a chrx-file and > apt-1.8.5 is used. I think --chrX-force has been superseded by > --no-gender-force. > > 2) If apt-probeset-genotype fails it would be very useful if the error > message it produces would be propagated to users of the plugin. Now > the > plugin error message is "Unexpected exit of APT sub-process", which > could, for example, mean apt-probeset-genotype failed with the message > "FATAL ERROR: Only 0 SNP clusters had enough information to generate > prior. Please try using more cel files." or "FATAL ERROR: Don't > recognize option: '--chrX-force'". > > cheers, > > Markus > > ------------------------------------------------------------------------- > 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/ > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel --- 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/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
