Gatins Set error
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0
Entering edit mode
@e130c182
Last seen 2 days ago
Israel

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
flowCore Bioconductor • 45 views
ADD COMMENT
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

GatingSet isn't a function in flowCore. It is however in flowWorkspace, which you would need to load first.

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