Hi,

We have been using flowcore, flowworkspace, and opencyto very successfully for our mass cytometry data and are trying to apply it to our flow data. We have successfully been able to use this pipeline with out macsquant data that is converted from mdq to fcs in flowjo but I have been trying to export the fcs directly from the Macsquant machine to skip this manual step. I have successfully converted and gotten the fcs read in with read.FCS but have been running into issues when trying to transform this data. Does any have any recommendations on the output fcs settings from Macsquant and arguments for read.fcs that have allowed them to use these files?

Best, Taylor