FCS files can suffer from flaws introduced by the cytometer during acquisition. FlowJo can test the validity of selected samples in the Workspace, or of all samples as they are loaded into the workspace. You can adjust the sensitivity of the test to allow small measurement fluctuations. You can exclude parameters that are not pertinent to the current analysis.
Select samples of suspect validity in the Workspace. Open the utility from Platforms > Verify Sample Validity.
If you wish to test every subsequent sample, check the box in the upper left (red circle above.)
The samples you selected will be listed on the left. Sample 1 in the example above was highlighted, then checked individually by pressing the Check Sample Validity Now button. The black dot in the Chk? column indicates that it has been checked. Had it failed, there would also be a dot in the Fail? column.
Sample 3 is highlighted and ready to be checked by the same procedure.
Clicking Show Time Plots opens the window below. For more on this tool, click here.