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 when the layout is reopened. When working with large data sets or computationally intensive transformations the team at De Novo Software recommends saving/exporting a new .FCS file that contains the newly calculated tSNE X and tSNE Y parameters so you may more easily work with the data set without having to recalculate the tSNE results.

 

Exporting/Saving the newly create tSNE X and Y Parameters as part of a new .FCS file is easily 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 create is saved so you may review the settings used to create the tSNE transformation at anytime in the future.