cytofkit2 error: "Selected marker(s) is/are not in the input fcs files"

[tsneplotter]

Hey everyone,

I'm trying to use cytofkit2 to analyze some Mass Cytometry data, but I keep getting the error "Selected marker(s) is/are not in the input fcs files". I've checked the marker names carefully, and they seem to match the column names in my FCS files. I've also made sure that all the markers are of type "numeric".

Here's the code I'm using:

R
library(flowCore)
library(cytofkit2)

Load FCS files

fcs_files <- c("C:/Users/PC-Neu/Desktop/2314.fcs", "C:/Users/PC-Neu/Desktop/2315.fcs")
fcs_data <- lapply(fcs_files, read.FCS, truncate_max_range = FALSE)

Assign marker names

marker <- colnames(fcs_data[[1]])

Run cytofkit

cytofkit_output <- cytofkit(fcs_files[1], fcs_files[2],
markers = marker,
transformMethod = "cytofAsinh",
mergeMethod = "all",
dimReductionMethod = "tsne",
visualizationMethods = "tsne")
Verwende den Code mit Vorsicht.

I've tried the following things:

Updated cytofkit2 and all dependent packages to the latest versions.
Restarted R to make sure there are no conflicts with other packages.
Checked the marker names for any invalid characters.
Tried loading the FCS files individually with read.FCS().
Simplified the marker vector to include only a few markers.
None of these things have worked. I'm still getting the same error.

Here is the output of flowCore::markernames(fcs_data[[1]]):

flowCore::markernames(fcs_data[[1]])
Time
SSC-H
SSC-A
FSC-H
FSC-A
SSC-B-H
SSC-B-A
BV421-A
Pacific Blue-A
BV510-A
BV570-A
BV605-A
BV650-A
BV711-A
BV750-A
BV785-A
Alexa Fluor 488-A
Spark Blue 550-A
Spark Blue 574-A
PerCP-Cy5.5-A
PE-A
Spark YG 581-A
PE-Dazzle594-A
PE-Fire 700-A
PE-Cy7-A
PE-Fire 810-A
APC-A
Alexa Fluor 647-A
Spark NIR 685-A
Alexa Fluor 700-A
Zombie NIR-A
APC-Fire 750-A
APC-Fire 810-A
And here is the content of my marker vector:

print(marker)
[1] "Time" "SSC-H" "SSC-A" "FSC-H"
[5] "FSC-A" "SSC-B-H" "SSC-B-A" "BV421-A"
[9] "Pacific Blue-A" "BV510-A" "BV570-A" "BV605-A"
[13] "BV650-A" "BV711-A" "BV750-A" "BV785-A"
[17] "Alexa Fluor 488-A" "Spark Blue 550-A" "Spark Blue 574-A" "PerCP-Cy5.5-A"
[21] "PE-A" "Spark YG 581-A" "PE-Dazzle594-A" "PE-Fire 700-A"
[25] "PE-Cy7-A" "PE-Fire 810-A" "APC-A" "Alexa Fluor 647-A"
[29] "Spark NIR 685-A" "Alexa Fluor 700-A" "Zombie NIR-A" "APC-Fire 750-A"
[33] "APC-Fire 810-A"
Does anyone have any ideas what could be causing this error?

Thanks in advance for your help!

tsneplotter