In order to export new FCS files based on the events within nodes within bubbles, bubbles must first be created.
After bubbles are created, select the bubble names in the sidebar to the left, under the box that says Event Export...Select Bubbles To Export, and click Export to New Experiment. This will write the events in the selected bubbles into separate FCS files in a new experiment on Cytobank. A file will be written for each bubble times each FCS file in the analysis. For example, in an analysis with five files and four bubbles selected, the result will be twenty new FCS files.
(The bubbles present in the SPADE analysis are listed. Highlight the ones to export and then click the link. The result will be a number of newly written FCS files equal to the number of bubbles times the number of files)
When the new files are written, the file names will be appended with which bubble the events originated from (see below).
(the new files are written with the name of the bubble the events originated from appended to the end of the file)
Consider using cluster gating of the exported SPADE files to open up useful downstream analysis visualization and workflows.
Because of this naming convention, Sample Tags can be used to quickly and easily annotate these files, and then the annotations can be used to drive figure generation.
The Export Statistics Tool can also be used to create a batched spreadsheet export of the files created from this workflow.