Hi all, We have released BASE 2.7.2. The release includes important bug fixes in the LOWESS plug-in shipped as a part of the BASE package. Some other improvement are also included in the release.
It is highly recommended at all BASE installations where LOWESS is used as a part of their analysis in BASE are upgraded to this release. More details on the LOWESS problem is given below. Note, we have not found any problems with the BASE1 lowess implementation and analysis made with BASE1 lowess in BASE1 or BASE2 are still valid. More information about the changes in 2.7.2: http://base.thep.lu.se/query?milestone=BASE+2.7.2&group=resolution Download from: http://base.thep.lu.se/wiki/DownloadPage We regret any inconvenience that the LOWESS bug may have caused, The Lund BASE team Text copied from the installation/upgrade chapter of the BASE documentation, http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1 This release fixes a serious bug in the LOWESS plug-in shipped as a part of the BASE package. The bug is found in all BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be calculated. All data that has been normalized with the BASE2 LOWESS plug-in prior to BASE 2.7.2 should be considered invalid and needs to be re-normalized with the fixed version. Downstream analysis steps that has used the incorrectly normalized data also needs to be redone. For more information about the bug see http://base.thep.lu.se/ticket/1077 BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that includes data normalized with the LOWESS plug-in. An administrator can use this utility to extract a list of all experiments/bioassay sets that needs to be fixed. The utility can also tag the name of the found experiments/bioassay sets with FIX LOWESS to make it easier to find data that needs to be fixed. The utility can't see any difference between data normalized with the old version and the fixed version. It will simply report all data that has been normalized with the LOWESS plug-in. Only use the utility a single time right after the upgrade to BASE 2.7.2. The utility is a command line program that should be executed on the BASE application (web) server. cd <base-dir>/bin ./onetimefix.sh lowess_warn -u <login> -p <password> -f We recommend running the utility as the root user. The -f option is optional. If it is included the found experiments/bioassay sets are tagged with FIX LOWESS, otherwise only a list with the information is generated. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
