5  Import Concatened .fcs

The app supports the use of a single .fcs file containing all the cells, along with additional columns for initial .fcs ID, clustering, and possible dimension reduction information (e.g., t-SNE, UMAP). This file will be linked to a metadata file generated by the user, which contains fcs ID information to identify the different initial sample IDs and groups of interest.

To load and concatenate data in the app, follow these steps:

  • Upstream analysis:
    • Prepare your .fcs file: Ensure that your .fcs file contains all the cells and the necessary additional columns for initial fcs ID, clustering, and possible dimension reduction information.
    • Create a metadata file: Generate a metadata file that contains .fcs ID information to identify the different initial sample IDs and groups of interest. This file should be in a compatible format, such as CSV or Excel.
  • Through app:

5.1 Clustering selection

  • Through app:
    • Once the data is loaded, use the app’s concatenation feature Extract Clustering Features to combine the data from the different samples and groups. This will create a single dataset that can be used for further analysis and visualization.