error while parsing workspace with fcs files

[IvanaOsredek]

Hello,

I've been trying to parse the workspace from FlowJo with my fcs files using GetFlowJoLabels function. However, I get this error message:

Parsing 0 samples
windows version of flowJo workspace recognized.
version X
Error in flowWorkspace:::.addGatingHierarchies(gs, pd, execute, isNcdf, :
no sample to be added to GatingSet!
In addition: Warning message:
In .parse.pData(obj = obj, keywords = keywords, sg = sg, keywords.source = keywords.source, :
Can't find the FCS files for the following samples:
9 days after sorting_60220_coGFP_002.fcs_10000

I am sure that I have provided the right path to my files and the workspace.
For some reason my workspace adds to the name of the file "_1000" extension (Original file name is 9 days after sorting_60220_coGFP_002.fcs) .
I have tried to parse the same ws and files using OpenCyto and it worked. As soon as I try with GetFlowJoLabes function it fails.

Could you please tell me where it goes wrong?

Kind regards

[SofieVG]

Hi @IvanaOsredek ,

My apologies for not getting back to you earlier. Could you let me know if you managed to figure something out in the end?

It is surprising that the OpenCyto approach did work but the FlowSOM code not, as it just calls the OpenCyto functions internally. Can you have a look whether you still have the issue with the current version of the FlowSOM code?
I am especially surprised that your output starts with "Parsing 0 samples", which seems to indicate an empty workspace.

The _10000 indicates the number of cells and is added by OpenCyto/CytoML, not something we do in FlowSOM, so I don't think this will be what caused the issue.

Kind regards,
Sofie