Hi, i am trying to use FlowSOM to automatically identify cell clusters in a normal bone marrow sample. I managed to create the SOM however i experienced some trouble when trying to parse the FlowJo file with the manual gates with the SOM. The code i used was the following:

#LMD files from Navios cytometer have 2 datasets. The second one is the raw data matrix without compensation, while the first one is the data matrix with compensation already applied. I worked with dataset 2.

ff <- flowCore::read.FCS('Bue018 cfu normal 00000337 431.LMD', dataset = 2)
comp <- flowCore::keyword(ff)[["$SPILLOVER"]]

#I changed the column names from the compensation matrix in order to match the names from the flowframe object.


colnames(comp) <- c('FL1-A', 'FL2-A', 'FL3-A', 'FL4-A', 'FL5-A', 'FL6-A', 'FL7-A', 'FL8-A', 'FL9-A', 'FL10-A')
 ff <- flowWorkspace::compensate(ff, comp)
transformList <- flowCore::estimateLogicle(ff, channels = colnames(comp), m = 7)
ff <- flowWorkspace::transform(ff, transformList)
fSOM <- FlowSOM(ff,
                compensate = FALSE, 
                transform = FALSE,
                scale = FALSE,
                colsToUse = c(5:14), xdim = 7, ydim = 7,
                nClus = 10)

p <- PlotStars(fSOM, backgroundValues = fSOM$metaclustering)
print(p, newpage = FALSE)
FlowSOMmary(fsom = fSOM, plotFile = "FlowSOMmary.pdf")

#Manual gating parse

N <- "C:/Users/usuario/OneDrive/Agus/Trabajo LMA/Normales/Bue018/export_Bue018 cfu normal 00000337 431.fcs"
wsp_file <- "C:/Users/usuario/OneDrive/Agus/Trabajo LMA/Normales/Bue018/Bue018.wsp"
cell_types <- c("Erythroid", "Granulocytes I", "Granulocytes II", "Granulocytes III", "Monocytes I","Monocytes II", "Monocytes III", "Lymphocytes", "CD34+ Lymph", "CD34+ My", "CD34+ Stem" )
gatingResult <- GetFlowJoLabels(N, wsp_file, cell_types = cell_types)

#Error: 
FCS file found for sample Bue018 cfu normal 00000337 431.LMD has incorrect total number of events. Sample will be excluded.
FCS not found for sample Bue018 cfu normal 00000337 431.LMD_720184 from searching the file extension: .fcs
Error: No samples in this workspace to parse!




sessionInfo( )
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default


locale:
[1] LC_COLLATE=Spanish_Argentina.utf8  LC_CTYPE=Spanish_Argentina.utf8   
[3] LC_MONETARY=Spanish_Argentina.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Spanish_Argentina.utf8    

time zone: America/Buenos_Aires
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.3.1

I suspect there is a problem with the LMD file format, however, I would be very grateful if somebody could help me with this error. ¿Has anybody got any experience with FlowSOM and LMD files?