Time and gating in Flowjo after normalization in R

[EzequielD-86]

Thank you for this amazing package. Performs really well in our Mass cytometry data, but I came across a few things that dont know how to solve. After normalization in R, I exported the files back to Flowjo, but all the events seem to be crushed at the beginning of the scale for the time. Also , intensities of the different parameters had changed, Idk if because the data gets exported normalized, but the gates I had are no longer useful. Any idea on how to correct this issues? Thanks a lot!

[AnneliesEmmaneel]

Hi,
I am glad that the package works for you!
I would recommend to first perform PeacoQC and then apply normalization on the files. Can you tell me which kind of normalization you tried out and what the specific steps are that you do in FlowJo? Do you include the time parameter as well when normalizing/ cleaning your data?