After applying a transformation (e.g. TSNE, UMAP or FlowSOM) to your merged data files, you may wish to perform analysis on the individual data files within the merged file. You may follow the steps in this article to unmerge the data files and run batch processing in FCS Express.

1. Select a plot with the transformation applied.
2. Click the Data tab > Save from Plot
3. Click the Yellow Filefolder button to choose where to save the transformed data files.
   
4. In the File name field, enter the desired prefix to add to each original filename.
5. For Save as type, choose the desired file format.

• • DNS Data Stream Files (.dns) is a unique format within FCS Express that allows for storage of special information like merged spectral parameters, Classification Identifier, or the FlowSOM or SPADE minimum spanning tree. The .dns format is recommended if you plan to load the exported files back into an FCS Express layout later.
  • While FCS File format is a standard format for Flow Cytometry data, it only allows storage of numeric parameters. Merged spectral parameters will be lost, Classification Identifiers will be converted to numeric values, and FlowSOM and SPADE trees will not be viewable on the Plate Heat Map. This option can be used if you need to load the exported files into a software package other than FCS Express.

6.  Click Save

7.  For Save Split on Classification, choose Classification Identifier. This will split the merged file into individual files, preserving the original filenames.

8.  Keep all of the other options and fields as they are by default.

9.  If you scroll to the bottom of the parameter list, you'll notice that the transformed parameters (e.g. UMAP1, UMAP2, FlowSOM parameter)s will be included in the exported files.

10.  Click OK to begin the export.

11. Navigate to the save location to find the files.

12.  Load them into FCS Express as desired. We recommend loading them into a new layout without any transformations present.

• • Alternatively, if there are other plots you wish to preserve/use in the existing layout you can save a copy of the existing layout and delete the transformations from the transformations window.
  • We won't want the transformations to recalculate on the new files.
  • If you delete the transformation, and load the saved data file, you may need to adjust the parameters on the plot axes.