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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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Can't get GetFlowJoLabels() to match gating in FlowJo workspace #64

Open gmillerscripps opened 6 months ago

gmillerscripps commented 6 months ago

Hello, in the code below, I am getting the FlowJo labels from FlowJo using GetFlowJoLabels ( FlowSOM_2.8.0). The data come from https://flowrepository.org/id/FR-FCM-Z2TQ

Example file: 21-10-15_Tube_011.fcs

FlowJo workspace: General_panel.wsp

# 20.(B) Check the consistency with manual labeling
# 20.(B)(i) Extract the gating information from the wsp file
gating <- GetFlowJoLabels(files = "21-10-15_Tube_011.fcs",
                          wspFile = "General_panel.wsp")

I can't get table(gating$manual) to reflect what I am seeing in the FlowJo workspace. Some of them match, but not all. I had the same issue on my own dataset. Is there something I am not understanding about the use of GetFlowJoLabels?

Thanks!