geWorkbench

General

• Filtering a dataset to remove values marked as "missing" 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.

geWorkbench 1.8.0 and possibly all other versions

• Nov. 13, 2009 - it appears that geWorkbench does not run on a desktop/laptop installation of Linux, due to an incompatibility of the Java JRE with the GTK components used in Linux distributions. geWorkbench does run fine on a remote Linux server with the display using Cygwin X-windows on a Windows computer. Tests are continuing to find a solution.

geWorkbench 1.7.0

• Annotations - The retrieval of annotations using the Marker Annotations component does not work for microarray data downloaded from caArray. Bug 1956.
  • There is an easy work-around. After downloading data from caArray, and optionally setting up any needed groups of arrays or markers (e.g. treatment groups, controls etc), save the dataset as file type "Exp" format. You can then reload that saved dataset and associate the annotation file at that time.
• caArray - Data downloaded from caArray is being stored in a way that uses a large amount of memory, limiting the size of the dataset that can be used. Bug 1930.
  • The first work-around is to increase the amount of memory allocated to geWorkbench.
  • A second work around, if the first is impractical, is to download the data, using the "merge" check-box, in reasonable sized sets of arrays and then save each merged set as a separate "Exp" format file. Once saved, delete the downloaded data set in geWorkbench and then download the next set from caArray until all data has been saved to separate merged "Exp" files.
  • The Exp files can then be all read back in together and merged into a single data object (make sure to check the "merge" check-box).
• caArray - Data downloads from instances of caArray housed at the NCI can be very slow.