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I'm trying to analyze FACS data using the flowcore package and I'm getting an error when trying to generate the gating set saying the GatinSet function can't be found.
fs <- read.flowSet(path = "~/Library/CloudStorage/Box-Box/UlitskyLab/Projects/Sanofi_LNPs/Experiments/Luciferase/15_7_24_transfection_LNPs/",pattern = ".fcs",alter.names = T)
pData(fs)[1:3,]
#change names
colnames(fs)
colnames(fs)[colnames(fs)=="FL5.A"] <- "GFP"
colnames(fs)[colnames(fs)=="FL2.A"] <- "DNA content"
#gates
gs <- GatingSet(fs)
# gs <- GatingSet(fs)
Error in GatingSet(fs) : could not find function "GatingSet"
# please also include the results of running the following in an R session
sessionInfo( )
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS 15.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Asia/Jerusalem
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flowCore_2.16.0 dbplyr_2.5.0 BiocManager_1.30.26
loaded via a namespace (and not attached):
[1] gtable_0.3.6 dplyr_1.1.4 compiler_4.4.1 ggsignif_0.6.4 tidyselect_1.2.1 Biobase_2.64.0 cytolib_2.16.0 tidyr_1.3.1 scales_1.4.0 RProtoBufLib_2.16.0 ggplot2_4.0.0
[12] R6_2.6.1 ggpubr_0.6.1 generics_0.1.4 Formula_1.2-5 BiocGenerics_0.50.0 backports_1.5.0 tibble_3.3.0 car_3.1-3 munsell_0.5.1 DBI_1.2.3 pillar_1.11.1
[23] rlang_1.1.6 utf8_1.2.6 broom_1.0.10 cli_3.6.5 magrittr_2.0.4 grid_4.4.1 rstudioapi_0.17.1 lifecycle_1.0.4 S4Vectors_0.42.1 vctrs_0.6.5 rstatix_0.7.2
[34] glue_1.8.0 stats4_4.4.1 abind_1.4-8 carData_3.0-5 fansi_1.0.6 colorspace_2.1-2 purrr_1.1.0 matrixStats_1.5.0 tools_4.4.1 pkgconfig_2.0.3