Does converting channel value CSV to FCS remove the FlowJo-defined transformation?

[denvercal1234GitHub]

Hi there,

I want to use FlowJo to manually decide the transformation of the FCS files, so I exported the FCS as channel values after gating out debris, doublets and dead cells and adjust the biex axes.

But, I want to now use the peacoQC package (saeyslab/PeacoQC#14) to do the QC of my FlowJo-transformed data before inputting them back for clustering by Spectre.

So I plan to use the CSV-to-FCS script to convert my channel values csv files to FCS files in order for me to read them to the peacoQC package.

Would you mind letting me know whether this CSV-to-FCS script will remove the FlowJo-defined transformation?

Or, would you mind giving me some advice on how to best use peacoQC package together with Spectre? Because peacoQC only reads FCS or flowSet objects.

Thank you.