Affymetrix is already supported directly in your first install. You need to add plug-ins for normalization (and extracting data from the cel-files). There are two known places of Affymetrix plugins with some overlap
http://madr.lcb.uu.se/wiki/BasePlugins and http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix Look through these for the first steps. I reccomend to download the BASE document in pdf format and search for 'affymetrix' with shift-command-F. Go through the hit list. When you have created your first root bioassay you can use the built-in tools, find interesting plug-ins, or create new ones. You can also export bioassays in tmev format for import into MeV, http://www.tm4.org. MeV allows you to cluster and do a lot more with you data. Avoid using the MeV extension currently available for BASE since it is based on MeV 4.0 and the current MeV is 4.3. Cheers, Jari Moore, Jay wrote: > Thanks to all for the warm welcome to the community and help getting started. > I now have a working BASE installation on Mac OS X 10.5 server with Tomcat > 6.0.18 and Java 1.6, both as supplied by Apple as standard. > > Could I ask another question please? Does anyone have a recipe or hints for > setting up the extensions for a custom Affy chip (single-channel)? > > Many thanks in advance > Dr. Jay Moore > Warwick Systems Biology Centre > University of Warwick > > > > -----Original Message----- > From: Emil Lundberg [mailto:[EMAIL PROTECTED] > Sent: Tue 18/11/2008 12:18 PM > To: BASE ML > Subject: Re: [base] BASE on OS X server > >>> If you want to run it on older hardware (PPC or 32-bit), 10.5 still >>> helps. I do recall being told that BASE does not actually make use of >>> Java 6, it's just that they don't test on any older releases anymore, >>> but I'll let the BASE folks comment on that. You will have to >>> "compile" >>> BASE yourself though (see docs above, but basically "ant >>> package.bin" in >>> the source root, then follow the standard install instrux). >> The current version of BASE doesn't compile unless you have Java 6, so >> you'll need Java 6 to run it as well. I don't remember exactly in >> which >> BASE version this happened, but support for Java 5 was officially >> dropped in BASE 2.5, but I think it continued to work for a few >> version >> after that. >> >> We have some developers running on Apple's beta-release of Java 6. It >> seems to work, but not without some problems. I would not recommend it >> for production use. > > OK, great info! > > FWIW, Apple recently released the Java 10.5 Update 2 (updates java to > 1.6.0_07), so if you haven't already, give that a spin. > > I'd be most interested in the results, as we are planning to updating > BASE, too :-) > > >>> Further/up-to-date instructions (changing data root, creating the >>> db's >>> etc) should be provided by the output of the "port install" commands. >>> N.B. MacPorts does not currently provide a tomcat6 port, but as with >>> Java, likely the latest 5.5 is OK (BASE guys?). >> You will need Tomcat 6, since BASE uses features that are not >> available >> in Tomcat 5.x. Eg. Tomcat 6 has support for Servlet/JSP specification >> 2.5/2.1 while Tomcat 5 only has Servlet specification 2.4/2.0. But as >> far as I know, Tomcat is pretty platform-independent and you should be >> able to download and install Tomcat from http://tomcat.apache.org/. > > Ok, again thanks for the info. As I think I mentionend, 10.5 sever > includes tomcat 6, so we should be OK there, as 10.5/intel/64bit is a > requirement for Java 6 anyway. > > thx, > > /Emil > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
