Whilst OMIQ allows flexibility to design the Workflow which suits your analysis question, there are some patterns we generally find are unintentional.
If you have two nested Scaling tasks in your Workflow you could be transforming your data twice, which is generally not advised.
Consequence of Two Scaling Tasks
If you have two scaling tasks within your workflow, you are ArcSinh transforming your event values twice. This can result in very small values, likely to be less than 0.01 and can then round to 0.
You may still see the differences when plotting the data as these plots are just being scaled to reflect the smaller values. However, for outputs which rely on statistics (such as the clustered heatmap) you might see all your values as zeroes.
We would not recommend having multiple transformations of your data in a workflow. If you need a second Scaling task to change the minimum and maximum displayed you can select none (linear) and this will not apply a transformation.
For further context on scaling in Cytometry and OMIQ, we'd recommend taking a look at our scaling article!
Understanding Data Scaling - OMIQ
Example of the effects of multiple transformations on the same event.
We can see the first Arcsinh transformation usually brings the data down to around -1 to 9. The second transformation of the same data then makes the data very small and will have consequences on further analysis.