I am analysing a 14-parameter flow cytometry panel in FlowJo v10.3 and would like to clean up the data before analysis. There are two plugins (flowClean and FlowAI) which use R to get rid of bad quality data (e.g. interrupted flow or signal acquisition issues).
Despite following the tutorials, I am getting various error messages including:
"Could not create Gating-ML elements:
gating:RectangleGate
The target sample does not have some parameters referenced in the GatingML definition"
When this happens, I get some basic plots, but the programme does not split my "good events" from my "bad quality" events.
Alternatively "FlowJo could not derive the expected parameter" (ie the calculation fails totally).
Can anyone tell me why this is happening and how to fix it please?
I do not know your level of proficiency with the R programming environment, but I suggest you install the latest version of R (https://www.r-project.org/), R studio (https://rstudio.com/) and the FlowAI package (https://www.bioconductor.org/packages/release/bioc/html/flowAI.html) with the necessary dependencies.
Once you have done this (everything I described above is free), you just have to open R studio, digit "library(FlowAI)" to load the package and then the "flow_iQC()" command.
This will launch a shiny application that allows you to load your fcs files and perform an interactive QC on your flow data. You will get three tabs with: 1) flow rate, 2) signal acquisition and 3) dynamic range, which you can use to select high quality events. Once you are done, you can save the fcs file(s) with the highQ (or lowQ) events by clicking on the button in the lower left corner.
Finally, you can import your "clean" data in your favourite flow analysis software (FlowJo, FCS Express, etc..) or continue your workflow in R, depending on your needs.
Thank you- the reinstall worked (I have not tried the shiny app, but managed to run the cleanup in FlowJo, as well as do some analysis in R).
Hi Gabriele Casirati
I have the same issue as Zoya, with the "FlowJo has failed to produce the expected derived parameter" error message, even though i'm using the latest version of FlowJo (10.7.1) and R (4.0.3). However, I haven't downloaded Rstudio since it is never mentioned in any FlowJo video/tutorial talking about pluggins, do you think it could be the reason i have this error message ?
Thanks a lot for your help
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