Cannot create a GatingSet from my FCS files. Error: unable to find an inherited method for function ‘GatingSet’

[LuisaFJimenez]

Describe the bug
A clear and concise description of what the bug is.

Dear Team,
I am working with files from a Guava capillary flow cytometer. The format of the files is FCS2.0 and FCS3.0
with FlowCore functions I am able to create flowFrames and flowSets. However, when I want to create a GatingSet using the flowFrame object , I get the following error:

Error: unable to find an inherited method for function ‘GatingSet’ for signature ‘x = "flowFrame", y = "missing"’

I tried to see if it is a problem of my installation by following the instructions and code in your Vignette, under "0.4 Build the GatingSet from scratch".
I am able to create the GatingSet from the dataset included in the flowCore package (GvHD) as you described in your Vignette, but when I do it with my files, it does not work. It gives only the error I mentioned above.

Since the error seems to be associated with my FCS files, I will attached one of them here (FCS2.0)

AS_118_001.fcs.zip

I am including the session info

SessionInfo:
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Linux Mint 19.1

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so; LAPACK version 3.7.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] CytoML_2.16.0 openCyto_2.16.1 ggcyto_1.32.0 ncdfFlow_2.50.0
[5] BH_1.84.0-0 ggplot2_3.5.1 flowWorkspace_4.15.5 flowCore_2.16.0
[9] cytoverse_0.0.0.9000

loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 lattice_0.22-5 magrittr_2.0.3
[5] grid_4.4.1 RColorBrewer_1.1-3 jsonlite_1.8.9 plyr_1.8.9
[9] graph_1.82.0 gridExtra_2.3 fansi_1.0.6 scales_1.3.0
[13] XML_3.99-0.17 Rgraphviz_2.48.0 cli_3.6.3 rlang_1.1.4
[17] RProtoBufLib_2.16.0 crayon_1.5.3 Biobase_2.64.0 munsell_0.5.1
[21] yaml_2.3.10 withr_3.0.2 cytolib_2.16.0 parallel_4.4.1
[25] tools_4.4.1 dplyr_1.1.4 colorspace_2.1-1 BiocGenerics_0.50.0
[29] vctrs_0.6.5 R6_2.5.1 matrixStats_1.4.1 stats4_4.4.1
[33] lifecycle_1.0.4 zlibbioc_1.50.0 S4Vectors_0.42.1 RBGL_1.80.0
[37] pkgconfig_2.0.3 pillar_1.9.0 hexbin_1.28.4 gtable_0.3.6
[41] data.table_1.16.2 glue_1.8.0 Rcpp_1.0.13 flowClust_3.42.0
[45] tibble_3.2.1 tidyselect_1.2.1 rstudioapi_0.17.1 compiler_4.4.1

I thank you for your time,
kind regards,

Luisa

additional Info

• Gating works with the gating method on flowCore

rect_gate <- rectangleGate(list("FSC-HLog"= c(2.7, Inf), "SSC-HLog" = c(3, Inf) ), filterId = "Cells")
rect_gates <- sapply(sampleNames(singleFCS), function(sn)rect_gate)
p <- ggcyto(singleFCS, aes(x="FSC-HLog", y = "SSC-HLog")) +
  geom_hex(bins=216) +
  geom_gate(rect_gates)

• When I try to use the function load_cytoframe_from_fcs(), it "works" only when I add emptyValue = FALSE, but the created cytoframe has an empty matrix

[mikejiang]

wrap flowFrame into a flowSet, then pass it to GatingSet constructor