geWorkbench

Any current release

Installer - Versions of Norton Internet Security "Sonar" prior to NIS2011 may detect and delete a file generated during the installation process, "Install.exe". This will silently terminate the install. If this occurs, disable the Sonar feature during installation, or disable your antivirus protection during the installation.
PowerPC-based Macintosh computers - Java 6 is not available for the PowerPC platform, regardless of the version of OS X. For this reason, recent versions of geWorkbench which require Java 6 will not run on PowerPC Macintosh computers.

Gene Ontology Analysis - if a workspace containing a microarray dataset and its annotation information is saved and then restored, the gene ontology analysis will not work properly and should not be used.
Gene Ontology Viewer - In some cases when browsing the GO tree, when you select a particular term and view its associated genes, the list contains the "no gene name" entry (---). If this list is in turn copied to a marker set, the "---" will cause all matching markers, that is, those with no gene names, to be included in the new set.
- Workaround - use the "Multiple Entrez ID filter" to remove all markers that have no gene name associated with them.
- Fixed in version 2.2.2.

For issues with previous releases, please see the page Previous Release Issues page.

Filtering a data set may after an analysis has already been run may invalidate objects that arose from the original, unfiltered dataset. Any filtering should be done before any analysis which creates child result nodes, e.g. a t-test, ANOVA etc.