Hello everyone,

I'm trying to analyse flow cytometry data with the flowCore R package (with the goal of using the CytoExploreR package later in the analysis). My data is in fcs 3.1 format, exported from MacsQuantify software. When I run the function read.FCS() on my file, an error comes up :

> data <- read.FCS('data.fcs', emptyValue = TRUE)

Error: Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!)

Therefore, I change to emptyValue = FALSE and my file gets read just fine (in appearance at least). I can plot my data and it appears consistent with what I saw on the machine. But when I try to save this as a .fcs file (which I need for further analysis), I get this error

> data <- read.FCS('data.fcs', emptyValue = FALSE)
> write.FCS(data, 'data_2.fcs')

Error: Invalid input type, expected 'character' actual 'NULL'

I get the same error when I replace every occurrence of '//' in the file by '_', as suggested here -> https://github.com/RGLab/flowCore/issues/75 (Though I don't need emptyValue = FALSE anymore, so probably the double delimiter is not the problem at all?) I get similar errors when formatting the file as a flowSet rather than a flowFrame, or when using the function cyto_save() from the CytoExploreR package.

Thank you very much in advance, Sorry if I'm not precise enough, this is my first post. I may be able to share a file if needed, but the ones I have currently at my disposal are too big to be shared.