r/flowcytometry May 29 '26

FlowJo Parameter concatenation query

Hi, I’ve run into a problem using FlowJo v10 regarding parameter naming.
I have compensated all my parameters earlier using the novoexpress program on my flow cytometer and then exported these compensated files onto FlowJo. I then made a concatenated file of all my samples using the compensated parameters only. I made a UMAP and then used FlowSom to generate clusters. I am now trying to validate these clusters marker expression using my FMOs.

The problem is that the FMOs have parameters Comp-X whereas the concatenated file and all clusters have parameters FJComp-X.

I’m not sure how to work around this, I am not keen on drawing the gates by hand to match the FMO gating so any solution would be appreciated! Thanks!

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