how to get MFI stats from data
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@Khai-Chuong-24452
Last seen 27 days ago
United States

Hi,

I am a newbie to flow cytometry and R and trying to get MFI stats from my data. I tried following this wiki: wiki. I also looked at this resource: pdf. When I run the gs_pop_get_stats() it gives me an empty/Null data.table. When I tried doing it manually in FlowJo, I am able to get MFI and rSD. I would like both using R, is this possible? I'm probably not understanding a basic principle, would anyone be kind enough to educate me? Thanks.

one of the FCS files:

fcs file

My attempt:

library(flowCore)

parentpath <- "parent/path"
subfolder <- "subfolder_name"

fcs_files <- list.files(paste0(parentpath, subfolder), pattern = ".fcs")
fs <- read.flowSet(fcs_files)
gs <- GatingSet(fs[7])
rect.g <- rectangleGate(filterId = "main", list("FSC-A" = c(100000, 170000), "SSC-A" = c(30000,62000)))
rect.g2 <- rectangleGate(filterId = "sec", "V-450-A"=c(1.5e4, 4.8e4))

gs_pop_add(gs, rect.g)
gs_pop_add(gs, rect.g2)

recompute(gs)
autoplot(gs, "main")

gs_pop_get_stats(gs, "sec", type = pop.MFI)

>>Null data.table (0 rows and 0 cols)

sessionInfo( )

R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] rvg_0.2.5                officer_0.3.18           magrittr_2.0.1           ggcyto_1.14.1            flowWorkspace_3.34.1     ncdfFlow_2.32.0          BH_1.75.0-0             
 [8] RcppArmadillo_0.10.4.0.0 ggplot2_3.3.3            gridExtra_2.3            flowCore_1.52.1         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          lattice_0.20-44     png_0.1-7           assertthat_0.2.1    digest_0.6.27       utf8_1.2.1          R6_2.5.0            plyr_1.8.6          stats4_3.6.0       
[10] evaluate_0.14       pillar_1.6.0        zlibbioc_1.32.0     gdtools_0.2.3       rlang_0.4.10        uuid_0.1-4          rstudioapi_0.13     data.table_1.14.0   Rgraphviz_2.30.0   
[19] hexbin_1.28.2       flextable_0.6.5     rmarkdown_2.7       labeling_0.4.2      stringr_1.4.0       munsell_0.5.0       compiler_3.6.0      xfun_0.22           pkgconfig_2.0.3    
[28] systemfonts_1.0.1   BiocGenerics_0.32.0 base64enc_0.1-3     IDPmisc_1.1.20      htmltools_0.5.1.1   tidyselect_1.1.1    tibble_3.1.1        matrixStats_0.58.0  fansi_0.4.2        
[37] flowViz_1.50.0      crayon_1.4.1        dplyr_1.0.5         withr_2.4.2         MASS_7.3-54         grid_3.6.0          gtable_0.3.0        lifecycle_1.0.0     DBI_1.1.1          
[46] scales_1.1.1        RcppParallel_5.1.3  graph_1.64.0        KernSmooth_2.23-20  zip_2.1.1           stringi_1.5.3       renv_0.13.2         farver_2.1.0        latticeExtra_0.6-29
[55] xml2_1.3.2          ellipsis_0.3.2      generics_0.1.0      vctrs_0.3.8         RColorBrewer_1.1-2  tools_3.6.0         Biobase_2.46.0      glue_1.4.2          purrr_0.3.4        
[64] jpeg_0.1-8.1        parallel_3.6.0      colorspace_2.0-0    knitr_1.33         
>
flowCore flowStats flowUtils flowWorkspace • 83 views
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