The Gate's Axis Scale

In FCS Express each gate retains the axis scale that was on the plot at the time the gate was drawn.

When exporting gates to GatingML:

• If the gate's axis scale is Linear, Log with Negative, Lin/Log, or Hyperlog, the scale gets exported as the Linear type.
• If the gate's axis scale is Log, the scale gets exported as the Log type.
• If the gate's axis scale is ArcSinh, the gate's scale gets exported as the ArcSinh type.

All of these axis scales are valid for GatingML.

• If the gate's axis scale is Biexponential, the scale gets converted to the Logicle type.
• The Logicle scale formula is only valid if the Below Zero Parameter is high enough.

If you encounter a warning message when attempting to export gates to GatingML, the gate's axis scale is the biexponential type, and the Below Zero Parameter is too low for valid conversion to the Logicle type.

Make a note of the gate that is mentioned in the warning message and then follow the procedure below.

How to set a valid scale

There are two options for setting a valid scale formula.

Option 1: Increase the Below Zero parameter for the problematic axis (take the X axis, for example, in the pictures below).

The current Below Zero Parameter can be found in the Axes category of the plot's formatting menu

To increase the Below Zero parameter:

• uncheck Automatic
• select Use the value
• Enter a value that is sufficiently high. *Setting the value above 15 is sufficient for most data files*.

As a reference, the minimum acceptable Below Zero Parameter value is listed for a few data types in this table:

Please note: Assigning a low value to the Below Zero parameter can cause a single population to appear separated around Zero. See the example below:

Option 2: Change the scale type for the problematic axis to something other than Biexponential.

In the Axes category of the plot's formatting menu, under Scale, select a different scale type from the dropdown menu.

Redraw the affected gate(s)

After making the adjustment, you will need to redraw the problematic gate. The gate's axis scale will then match the new axis scale on the plot.

• Click the Gating tab
• Choose the desired gate shape (e.g. Polygon, Rectangle)
• Draw the gate on the plot over the existing gate.
• Select Replace an existing gate
  • From the dropdown menu, select the gate you are replacing
  • Click OK

Now the gate can be successfully exported to GatingML.