One of the most frequently questions I'm asked is, "Why does the data look different in FlowJo as compared to DIVA?"
It is a result of the biexponential transformation.
DIVA calculates the "best" transform and typically uses a width basis around -100 by default. Therefore, the first two decades are compressed into the linear space around 0.
Since the fcs3.0 standard does not include a keyword for exporting the transform used, it is up to the analysis program to apply the transform to the data.
FlowJo's default is set at -10 by default. Hence, only the first decade is compressed into the linear space. This leads to a difference in the visualization of data between DIVA and FlowJo.
We encourage users to start with a width basis of -10 and increase it if necessary. Too much initial compression can lead to the accidental loss of dim events because they are compressed into the negative population. While a width basis of -100 often makes the data appear 'cleaner', we recommend users start with a minor transform and scale it up as necessary. If you prefer to start with a default width basis of -100 in FlowJo, you can set it in the preferences.
For Mac: FlowJo>preferences>workspace tab>digital data
For PC: Edit>preferences>fcs3.0 scaling preferences
Other aquistion programs use different default transforms or no transformation. You can also turn the transform off in FlowJo by default if you prefer.
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