Using FlowJo gating on pre-compensated, pre-transformed FCS files about cytoml HOT 5 OPEN

Not that I'm aware of a the moment. flowJo to gating set conversion was built for importing data analyzed using a standard widespread workflow from flowJo, it makes some assumptions about what that workflow is, including that that data has been transformed and compensated in flowJo.

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Your error message seems to be indicating something wrong with fcs files you feed to this converter, which could be due to the reason Greg mentioned. Is the fcs written by flowcore or flowjo? Feel free to share the reproducible example data for troubleshooting

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The FCS file is written by FlowCore and is like I said pretty abnormal (e.g., no spillover matrix etc.) compared to a regular FCS file. Unfortunately I cannot share the file due some restrictions in this study. However, I think any FCS file generated by the AggregateFlowFrames function of FlowSOM would result in the same errors..

I managed to solve my issue by using execute=FALSE after which I wrote a small script to browse through the gating hierachy in order to get the correct labeling based on the leaf nodes. Do you know of any functions that can do the same thing? My implementation works but I would like to use something a bit less "hacky".

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maybe you can try to export fcs from flowjo, and use that together with wsp file to see if that works. I am not asking for the original data, any reproducible example will help us to further assist you

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Could you send directly to Mike a FCS with 20 events? I don't think this will reveal much of you study.

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