Sometimes huge data sets can cause out of memory errors. For some algorithms (notably HCL), we get out of memory errors if the number of genes is larger than about 10,000.
Data filters are available in the menubar under Adjust Data -> Data Filters. See the user manual for more information on data filtering.
If you are using a PC or a Linux machine, you can edit the TMEV.bat file (the file that you double-click on to start MeV) in a text editor and change the memory allocation. To this, find the text "java -Xmx512m" in the file, and replace 512 with 768 or 1024.
If you are using mac, click on Mev_MacOSX_2_2. Select "show package contents". Open 'contents' folder. Click on Info.plist. Open it in a text editor. You will see the following key and related string in the file:
Just change the 512 to 768 or 1024 and save the file.
Whatever platform you are using, be sure to allocate less memory to Java than the total amount of memory on your system. If you try to give Java 1024Mb of memory on a system that has only 512, MeV will not start.