Transformation Differences

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.

- Question or comments can be sent to nick@treestar.com

 

 

Comments

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