Some files cannot be directly opened in FlowJo.  These include the compensation matrix files and exported data files that it creates.  In order to read in a data file, create a new workspace (or open an existing workspace), and use the "Add Samples" command.  To load a compensation matrix, selected the "Compensation..." menu item, and choose "Load matrix..." from the submenu.

For more information about reading data files, click here.

For more information about compensation, click here.