Known Issues
geWorkbench 1.7.0
The retrieval of annotations using the Marker Annotations component does not work for microarray data downloaded from caArray. Bug 1956.
geWorkbench 1.6.0
A preliminary version of geWorkbench was released on October 20, 2008. A final version will be released on October 23, 2008. This update fixes problems with grid services, pattern discovery, and t-test. You can check the release date on the geWorkbench Help-version tab.
geWorkbench 1.5.1
The current release of geWorkbench is 1.5.1, dated September 23rd, 2008.
Issues in previous releases can be reviewed by examining the release notes, which are available at http://gforge.nci.nih.gov/frs/?group_id=78 by clicking on the release name.
No annotations loaded when data downloaded from caArray
When data is downloaded from caArray directly into geWorkbench (via the "remote file" option) the user is not prompted to associate an annotation file. This feature will be added in a future release.
Connectivity with caArray 2.1.0
The new release 1.5.1 of geWorkbench includes updates to allow it to connect with NCI's caArray 2.1.0 and caCORE/caBIO 4.0/4.1.
Previous releases, including 1.5.0, cannot connect with these updated services.
(The production caArray instance at NCI was upgraded to Release 2.1.0 as of August 12th, 2008).
The problems previously seen with Linux distributions should no longer occur. As of release 1.5.1 geWorkbench is now packaged using InstallAnywhere 2008, which corrects the previous problems.
genSpace component
In geWorkbench 1.5.0, the genSpace component, which (optionally) reports usage statistics to a central server, was not configured correctly in the file all.xml. This is fixed in release 1.5.1.
Clustering - Limitations/Requirements
In version 1.0.4+, the Hierachical Clustering tutorial requires a machine with 1 GB of memory, and the Java heap size must be set to at least 450 MB. This can be done in the file UILauncher.lax which is found in the application root directory of the InstallAnywhere packaged versions of geWorkbench. Specifically, the following line in that file should be set as follows:
lax.nl.java.option.java.heap.size.max=450678989
Version 1.03 of geWorkbench and earlier used an algorithm for Fast Hierarchical Clustering which did not implement the commonly understood versions of Average Linkage and Total Linkage. We do not recommend further use of that version.
