process_fcs() : Error 'x' must be an object of class flowFrame

[ppreshant]

I'm trying to use flopR to analyze a few .fcs files for the automated features it provides. I have installed the package using devtools::install_github() and ensured the prerequisites c("flowCore", "flowClust", "flowStats") are installed.

When I try to run one .fcs file at a time from the dataset using process_fcs(_fcspath_, flu_channels = 'mScarlet-I-A', do_plot = T)

I get the output -

[1] "2 clusters found"
[1] "only debris found"
Error 'x' must be an object of class flowFrame

and some additional warning messages reg NaNs and fluorescent channel exceeding saturation

How do I go about troubleshooting this since no additional information is given about the function generating the error?

I am able to read and visualize the same files using flowWorkspace::'s cytoset and cytoframe datatypes like this -

The .fcs file is attached here -
E01.zip

Desktop:

• OS: Windows 10
• R Version : 4.1

[ajfedorec]

Thanks for bring this to my attention. The error was due to the way I was handling "debris". I've now removed the "debris only" classification as it was just based on some hardcoded thresholds which weren't universally relevant.

Can you reinstall flopr with devtools::install_github('ucl-cssb/flopr') and try again?

Thanks for your patience

[ppreshant]

That has done the job, thank you!