Adding Samples
To analyze samples, you must first create a new workspace and then add the sample files to this workspace. Add samples by clicking on the Add Sample button in the workspace (leftmost function button).
You will be shown the standard Macintosh Open File dialog. You can add a single file by opening that file directly. If FlowJo determines that this is an FCS file, it will read it in and add it to the current group.
Alternatively, you may select a folder and click on the button Add all files in folder. FlowJo will then look at every file in the folder you specify. If it is an FCS file, it will be added to the workspace. In addition, FlowJo will create a new group that has the same name as the folder you selected; the files you just read in will be added to the folder. This way you can add an entire experiment at once!
Finally, if you select the button Add all files in all folders, FlowJo will look within the folder you select and (1) add all FCS files in that folder; (2) search within each folder contained therein for FCS files and add them; and (3) continue this search as deep as possible (i.e., looking for data in folders within folders).� Each time a data file is encountered, FlowJo will create a new group with the name of the folder that the data file is in and put the data file in that group.
Note: You can also add sample files (or folders of sample files) by simply dragging and dropping the files from the finder to the workspace window.