Why is my geometric mean always zero?

The Geometric mean is defined only for Positive Values. A more detailed definition can be found on Wikipedia. That means that if there is single cell with a value of zero, or below zero, the Geometric Mean will be undefined. When this happens, FCS Express displays a zero as the statistics result. Zero or negative values in your data can often happen counterintuitively as a result of compensation. In this case, the only way to have a valid geometric mean is to eliminate the negative values by creating a gate on the positive only values and applying the gate. You can then get a valid Geometric Mean on those positive values.