### Starting MultiExperiment Viewer

If using Windows, run the TMEV batch file (TMEV.bat) to start the program. Similarly, if using Linux or Unix, run the tmev.sh file. Macintosh users should double-click on the application file named MeV. Be careful not close the window to the command prompt window or else the whole program will close.

A main menu bar will appear, with five menus: File, Display, Window, About and Help. A Multiple Array Viewer should also open. To open a new Single or Multiple Array Viewer, load a new preferences file, or log in to a database, use the File menu in the main menu bar,. MeV will continue to run while this menu bar is present. To exit the entire application, select Quit from the File main menu.

Expression data can be viewed from within either a Single or a Multiple Array Viewer. However, the former can open only one set of expression data at a time. The Multiple Array Viewer can display many samples together. The real power of MeV is in the program’s analysis modules, found only in the Multiple Array Viewer. That is where the clustering and visualization of data can take place. Therefore, the remainder of this manual will focus on the Multiple Array Viewer. Please see section 2 for details regarding the Single Array Viewer.

#### Using Java Webstart

Another way to start MeV is by launching it via Java WebStart. In this way, MeV can be launched from a web page by clicking a link. A pre-selected data set and annotation can be automatically loaded without user intervention. Setting up this sort of system is the responsibility of the web site’s administrator, and so is beyond the scope of this manual. More information and technical details about this feature and MeV’s command-line options are available at http://www.tm4.org/mev_webstart.html.