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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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Cannot overwrite fcs files when re-load old data #83

Open roelar opened 4 years ago

roelar commented 4 years ago

Hello: I am trying a different annotation for the Rphenograph clustering in Shinyapp but when I try to save the new annotation files I don't see new fcs files or the updated version of the old fcs files. It seems to be a problem with finding the original files to overwrite. This is the message I get:

/var/folders/8l/1lyl6pp91gd4y13wgg1t33qs2c6gtc/T//RtmpEtgtl2/5eec6fa99cb99ee93af15196/0.RDataWarning in eval(expr, env) : Path for original FCS files doesn't exist, data cannnot be saved to new copies of FCS files.Please check path: /var/folders/8l/1lyl6pp91gd4y13wgg1t33qs2c6gtc/T//RtmpbMciCe/dd196aa577b154f77dc7e5c0 Writing results Done! Results are saved under path: ./

Both, csv and .RData are generated, but there is no new folder of analyzed fcs files. Could you please indicate what could I change to fix this? I tried using different working directory with the original fcs files in it but still not working. Thank you very much!

SamGG commented 4 years ago

Hi, To export FCS files, the original FCS are needed and should be located at the exact same location when you did your first analysis of this set of FCS. I think... Best.