After performed LIMMA analysis (2 factor, 4 groups factor a, 6 groups factor B. I am not able to save the Mev analysis. Saving current Analysis window persist for hours (left on overnight only to come back to the same progress bar)with the blue progress line in continuos progress. I am using Windows XP, and the latest Java, I have also made the recommended changes to the tmev4.bat file (java -xmf -1024) . When I look at the command line window i get an out of memory error. Thanks for your help on this. Lamar
Unfortunately there isn't much we can do. As you noted it is simply running out of memory. Setting -Xmx to 1024 is not a sure fire solution, as you can clearly see.
I would recommend you to run it on a bigger box if saving the analysis is absolutely necessary and set the -Xmx to as much as you can on that box.
Thanks for you using MeV.
Another quick thing. if you want to just save the significant/non significant gene list(s), you can right click on the table views and see an option to save it to a file.