Knowledgebase - Why do I get the message that a data file exported from a FACSDiva™ Experiment is invalid?

Exporting from Diva

When you export an experiment from BD FACSDiva, an XML file containing the experiment is created, along with files with the extension .fcs.

  • In Diva version 6 or earlier, these FCS files will have a numerical name (i.e. 300.fcs).
  • In Diva version 7 or later, these FCS files will have a more descriptive name (possibly including the sample and/or tube name).
These files correspond to the samples and tubes in your experiment. They are intended to be used by FACSDiva itself in conjunction with the XML file, but are not for use alone with a third-party analysis tool. When used in any third-party software, including FCS Express, the contents of the files may not be accurate. For example, the compensation information in these FCS files may be different from what was in your experiment.

Therefore, when you want to export an experiment from Diva, you will need to take two steps:

  1. Export the experiment from Diva using the menu item File -> Export -> Experiments. This will export the experiment along with the set of invalid FCS files.
    • Delete these invalid FCS files, since they will not be used
  2. Export the data files from Diva using the menu item File -> Export -> FCS Files. This will export the correct data files, which will be named:
    • In Diva version 6 or earlier, Specimen_Tube.fcs (or, if it is a part of a place, Specimen_Tube_Well.fcs)
    • In Diva version 7 or later, there are several options for naming the files (see the Diva User Preferences image, on the right). Whichever options you select, make sure that you include both the specimen and the tube , otherwise FCS Express will not be able to load this file when importing an experiment.

Loading the files into FCS Express

Diva files can be loaded into FCS Express just like any other data files - by inserting a plot, and then selecting the file in a file dialog. For information on loading the entire experiment please see Importing a FACSDiva File.
By default, FCS Express will not create new plots for the invalid data files (exported using option #1 above) without your explicit approval.

If you try to open a new plot, and use one of these files, you will see a message like this:

If you have access to Diva and the original experiment, we recommend going back to Diva, and exporting the FCS files as described in step 2 above. However if you do not have access to Diva to perform the second export, or you have already deleted the experiment from Diva, then you will need to open the numerically-named files.

In that case, in FCS Express, access default Options (via File tab > Options), and then in the Data Loading > FCS File Options category, check the checkbox for Allow opening BD FACSDiva data files that were generated by exporting a FACSDiva Experiment.

After checking that checkbox, you will be able to use the numerically-named data files without any problem in FCS Express. Once again, we would like to stress that these data files may not be correct and HIGHLY recommend exporting the data files as described above in the future. Note that if you have turned on the checkbox, and have loaded a data file but are not certain whether it was exported using with the experiment, or as an FCS File, please check the first parameter. If the first parameter is Time, then it was exported with the experiment.

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