Some flow researchers with large event count files, ask us for tips to speed up the FlowJo analysis. Here are a couple quickies.
If the analysis workflow allows it, one can do some pre-processing. In FlowJo, gate on Cells of interest (eliminating debris and doublets), then use the Export feature to create smaller fcs files.
One can benefit from setting up a RAM disk, especially if the fcs files are greater than 10MB. (If you need more RAM for your Mac, check out www.crucial.com). On MacOSX, one can mount a 2Gig RAM Disk easily by pasting the text below into Terminal:
diskutil erasevolume HFS+ "ramdisk" `hdiutil attach -nomount ram://4000000`
Or one can use a program like Tmpdisk to create a RAM Disk.