For those of you who would like to export your files out of FlowJo (for Mac) as new .fcs files, you may have come across a nagging little bug: your file names ($FIL) get cut short and no longer make sense. A workaround is presented here to ease the headache.
The key? Assign a separate set of keywords that you can use after exporting to orient yourself to the proper sequencing of your sample set. To save time add these keywords at acquisition, but in case this step was passed up, the example below will show how to add the the keywords in FlowJo.
To add the keywords in FlowJo (for this example, Tube Name and Tube Number), go to Workspace=>Add Keyword. A new Workspace column will appear with each keyword added. Type the keyword into the first cell and then copy/paste that word into each cell in the column (alternatively, use a spreadsheet to copy/paste an entire column of cells into FlowJo).
If you are going to use keywords you assigned at acquistion, throw them into the Workspace from by adding columns from the Edit button.
Then create a value series (in this case, 1 to 5) by typing in 1 (or any other number) in the top cell of the Tube Number column. With your cursor still in that column, go to the Workspace menu, hold down the Option key and select Create Value Series from the options. You can then create a numerical value series however you would like. 1-16, 100-150, etc.
After doing these steps, my workspace has the two columns I added:
Change the name that FlowJo displays in the workspace "Name" column
in preferences (go to Workspace=>Workspace Preferences). If you
already set up keywords during acquisition (best practice), it is very
easy to sel
ect a combination of keywords that you would rather have displayed instead of the $FIL keyword (aka data file name).
In my workspace, I made two new keywords with named Tube Name and Tube Number. I can then export everything with the file name Tube_1 through Tube_5.
After exporting as a new .fcs file (Workspace=>Export) I added the samples back into FlowJo and here is what is displayed in the Name column:
Granted this isn't the most elegant solution, but the "frustration savings" should more than offset the cost.
For more on Exporting, go here: http://www.flowjo.com/v8/html/export.html
content credit: Nicholas Ostrout
editing credit: Ryan Farmer