Date: June 3, 2005 at 3:34:35 PM
Subject: GeneTraffic upgraded from version 3.2-1 to 3.2-11

GeneTraffic has been upgraded to the latest version. Below are the release notes for versions between 3.2-1 and 3.2-11:

3.2-11
* added option in significance analysis to search for 'probe set ID contains text' in addition to 'probe set ID equals'
* one color project MAGE-ML export in project summary zip file changes
* files can now be loaded into ArrayExpress
* under the MAGE-ML folder, there is one xml file to hold the project structure and one or several txt files, holding data for the xml file
* Miscellaneous bug fixes:

* corrected a bug whereby exported Tif files were in gzip format and not able to be easily opened
* corrected a bug where centering would not process if table was being filtered without one of first 3 boxes checked
* corrected a bug where no Gene Identifier would show up when importing Agilent XML layout files
* corrected a bug where you could not process a table that had been created by uploading a gene list with extraneous IDs
* added missing icon for hybridization statistics page
* corrected performance counters showing 'NaN'
* corrected a bug that showed a mising annotation screen in two color project array layout screen
* corrected a bug where variance inflation would cause Diferential Expression value sign to be reversed in the vocano plot
* corrected a bug where the wrong text would appear at login time if a user is already logged in to the server
* corrected a bug where the logs for the month of December would not be displayed
* corrected a bug where a scheduled restart would not work
* corrected a bug where hybridizations could not be deleted
* corrected a bug where a project owner could be assigned as a co-author as well

3.2-3
* added the ability to change the name and description of data tables in the data management tree
* increased the limit on the number of search terms that could be used in spot/probe set query
* miscellaneous bug fixes:

* corrected a bug in choosing Geometric mean for baseline calculations
* corrected a bug in reading the .cel file during GC-RMA processing **
* corrected a bug wherein new Affymetrix projects would not produce annotations
* corrected a bug where users could not use the .Export to PathwayAssist. functionality for newer versions of PathwayAssist
* corrected a bug with an XML Doc error caused when importing gene tables with too many columns
* removed the limit on the number of GeneChips that could be loaded in QuickLoad

** due to an anomaly with Linux not stopping at the end of the file while reading the .cel file during GC-RMA processing, some users may have seen a discrepancy in their data between versions 3.1 and 3.2 of GeneTraffic. In certain cases the last value in the .cel file may have been read twice. If this was a relatively small value, then the user will see a marked difference in results between versions of GeneTraffic. This issue has been corrected an all values from GC-RMA are now correct.