The objective of visualizing data on a measured parameter is to evaluate the distribution of the sampled data.  The axis scaling on a plot only affects how data is displayed on the plot with statistics always derived from the raw data in FCS Express.  All data files, regardless of the scale that they were acquired with, can be displayed in any of the scalings supported by FCS Express.

Biexponential scaling is frequently used to analyze cytometry data because it is capable of displaying data that falls below zero.  When using Biexponential scaling, FCS Express automatically calculates the Below Zero Parameter (i.e. the transition point) and the Axis Minimum (Resolution) to display on a plot from the raw data when the Automatic checkboxes are selected. All data below the transition point value will be scaled as linear, and all data above the transition point value will be scaled as logarithmic.

The ability to automatically adjust plot axes based on the data displayed on the plot aims to avoid potential unexpected negative populations (usually caused by compensation/acquisition issues) that may be missed.

Due to the variability of the raw data (min and max values for the data sets which sometimes can include extreme outliers), the automatic transition point and Axis Minimum (Resolution) used to display biexponential scaling on the axis of a plot may change between data files.  In FCS Express, it is possible to set both the Below Zero Parameter and the Axis Minimum (Resolution) to display on the axes to "lock" the Biexponential scaling so axes do not appear to shift when working between different data files that could have vastly different settings when using "automatic" mode.

In FCS Express, the biexponential scale for a given plot can be locked in place using the Axis formatting dialog.

1. Double click on the plot to open the Format window or right click on the plot and select Format this plot > Axes.
2. If not already selected, choose Axes from the dropdown menu at the top of the Format window.
3. Uncheck the Automatic box beneath Scale.
4. Select the Use the Value radio button in the Below Zero Parameter section.
5. Adjust the value via the slider bar or by manually entering a value into the text box.
6. Uncheck the Automatically set the minimum value check box *Note: Step 3-6 will need to be repeated for the X axis.
The Biexponential transition point where the data goes from linear to log will now be fixed and not change between data files. By default, FCS Express automatically sets the minimum (Resolution) value on the axis. Set a fixed value for the axis minimum (Resolution) in the steps below.
7. Under Min/Max (Resolution), uncheck the box next to Automatic Minimum.
8.  Enter a value appropriate for the data in the field next to Custom Minimum. *Note: Steps 7 and 8 will need to be repeated for the X axis.
The Axis Scaling and Axis Minimum (Resolution) displayed on the axes will now be "locked" and will not change between data files.