FlowJo Workspaces and FCS Files - A Connection

It is good to note that FlowJo DOES NOT save your FCS files as part of the Workspace. Rather, FlowJo saves the relative path to a set of FCS files and accesses the files, as needed, each time a Workspace is opened.

To save yourself from headaches, save the workspace in the SAME EXACT FOLDER as your FCS files.

If your files move, the Workspace has no way of knowing this. If you have ever opened a Workspace and been prompted to locate FCS files, then you have realized that FlowJo does not save the FCS files with the Workspace. This is almost always caused by a change in the file path to the FCS files. A few examples of this are:

-An entire directory is moved from one network storage to another network storage

H:\\folder1\folder1_A\folder1_b\yourFCSfiles

becomes...

L:\\folder1\folder1_A\folder1_b\yourFCSfiles

- A folder in the file path to your files changes names

C:\oldfoldername\yourFCSfiles

becomes...

C:\newfoldername\yourFCSfiles

- A folder that contains the FCS files that the Workspace knows about was left at the office/lab

GOOD:\You wrap up work for the week, but plan to do analysis at home and save the Workspace to a thumbdrive that you'll open on your home computer on Sunday afternoon

becomes...

BAD:\You are prompted by FlowJo to make the 45 minute drive back to your office and save all the FCS files to the thumbdrive and drive back home before you can do the analysis, all the while missing your favorite Sunday afternoon activity.

To save yourself from headaches, save the workspace in the SAME EXACT FOLDER as your FCS files.

FlowJo doesn't store the FCS files with the Workspace for a few reasons, but namely because storing the FCS files with the Workspace would require that FlowJo duplicate all the information of your files, resulting in an extremely large file. For example, if you loaded 40 FCS files that were 1MB each, the resulting FlowJo file would be 40MB+.

Therefore, FlowJo saves the relative path to your FCS files.

To save yourself from headaches, save the workspace in the SAME EXACT FOLDER as your FCS files.

Not doing this will result in you needing to relink all your FCS files every time you move the files. If hard drive space is not a concern, the PC version (as of 7.5) allows you to save your workspace using the next generation file standard, ACS. This will save all the information from your FCS files and the workspace into a single (very large) file. However, if you have a terabyte of hard drive space, than this is probably not a concern. If your workspace looses the extension pathway, your workspace is not lost. Do not reanalyze your data. Either relink all your files or check this URL out for other methods of preventing a coronary ;-)