error in load_cytoset_from_fcs when emptyValue = FALSE

[Biomiha]

It seems that load_cytoset_from_fcs doesn't actually accept the emptyValue argument. When I read in a set of fcs files using read.flowSet(fcs_files, emptyValue = FALSE) this works but when I try the same with load_cytoset_from_fcs(fcs_files, emptyValue = FALSE), I get the following error:

Error_ in fcs_to_cytoset(sapply(files, normalizePath), list(which.lines = which.lines, : Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!

[Biomiha]

Just realised load_cytoset_from_fcs is actually part of flowWorkspace. Apologies.

[DillonHammill]

The CytoExploreR wrapper for this is cyto_load() which calls these functions internally. cyto_load() is called inside cyto_setup() to read in the files. All exported CytoexploreR functions are prefixed with cyto_. You can post this issue on flowWorkspace so that it can be fixed by the RGLab - double check the docs to see if the name of the argument has not changed.

[Biomiha]

I get the same issue with cyto_load, e.g.:

cyto_load(path = fcs_files, select = list.files(fcs_files, pattern = "fcs"), emptyValue = FALSE)

Error in fcs_to_cytoset(sapply(files, normalizePath), list(which.lines = which.lines, : Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!

[DillonHammill]

That is to be expected, the same function is being called.

Have you tried looping through the files individually and calling load_cytoframe_from_fcs(). Perhaps the argument is not being passed on to this function from load_cytoset_from_fcs()?

files <- list.files("fcs_files", full.names = TRUE)
cf_list <- lapply(files, function(file){load_cytoframe_from_fcs(file, emptyValue = FALSE)})
cs <- cytoset(cf_list)

[Biomiha]

I still get an error:

files <- list.files("fcs_files", pattern = "fcs", full.names = TRUE)
cf_list <- lapply(files, function(file){load_cytoframe_from_fcs(file, emptyValue = FALSE)})
cs <- cytoset(cf_list)

Error in parseFCS(normalizePath(filename), list(which.lines = which.lines, : Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!

[DillonHammill]

If read.flowSet() works just use this and then convert the flowSet to a cytoset if you need to:

files <- list.files("fcs_files", pattern = "fcs", full.names = TRUE)
fs <- read.flowSet(files, emptyValue = FALSE)
cs <- flowSet_to_cytoset(fs)

I would still file an issue on flowWorkspace as well, so that this can be fixed.

[Biomiha]

Yes. This works as well.

files <- list.files("fcs_files", pattern = "fcs", full.names = TRUE)
cf_list <- lapply(files, function(file){read.FCS(file, emptyValue = FALSE)})
cs <- cytoset(cf_list)

[DillonHammill]

For anyone else experiencing the same problem this has now been fixed. If you need this feature you will need the latest versions of cytolib and flowWorkspace.

[BenJCQuah]

Dear Dillon Hammill,

Thank you for your awesome better-than-flowjo flow Cytometry analysis package. Do you think you will ever have a pipeline for spectral unmixing like you do for compensation?

Thanks!

BQ