In FCS Express Version 7.08 and above, newly calculated tSNE X and tSNE Y parameters are saved within the layout.  Thus, upon re-opening a layout saved in 7.08 or above in which the tSNE transformation was already calculated, there is no wait time required to see the tSNE-X vs -Y plot parameters again.

 

In FCS Express Version 7.06 and below, newly calculated tSNE X and tSNE Y parameters are not saved within the layout or data file but are instead calculated automatically (or manually) and applied to plots/files each time the layout is reopened. When working with large data sets or computationally intensive transformations the team at De Novo Software strongly recommends resaving the layout in version 7.08 or above, so that the issue of wait time for recalculation is obviated.  If that is not an option, then you may save/export a new .fcs file that contains the newly calculated tSNE-X and tSNE-Y parameters to avoid the wait time for recalculation.

 

Exporting/Saving the newly create tSNE X and Y Parameters as part of a new .FCS file is accomplished by:

 

1. Apply the tSNE transformation of interest to a given plot.

2. Click on the plot to select it.

3. Click on the Data tab→Save/Load→Export from the ribbon to launch the Export Data dialog.

4. Select the additional tSNE X and tSNE Y parameters from the list of Parameters to Export.

5. Perform the export normally according to the full instructions at Exporting FCS File Data from a Single File.

 

It is also recommend that the layout in which the transformation was created is saved so you may review the settings used to create the tSNE transformation at anytime in the future.