FCS3.2 reading
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jarod ▴ 30
Last seen 9 weeks ago
United States

I am having problems with FCS3.2 format using some of the standard packages for fcs parsing. Packages were installed with Bioconductor on Feb 17 2024 and R 4.3.2. Was having problems even installing these packages, particularly CytoML, on earlier R versions.

Are there any other options for reading and parsing fcs and wsp files? I am trying to convert these file types to a table with all parameter and gating info for machine learning purposes.

> fc <- as_tibble(exprs(read.FCS(fcs,truncate_max_range = F)))
Warning message:
In readFCSheader(con) :
  The flowCore package does not fully support FCS3.2 yet
> fc <- fc %>% mutate(imageid = paste0("id", sprintf("%0.8d", 0:(dim(fc)[1]-1)))) #Add imageid
> gs  <- flowjo_to_gatingset(open_flowjo_xml(wsp, sample_names_from="sampleNode"), name = 1) #flowWorkspace package
Error: This does not seem to be a valid FCS2.0, FCS3.0 or FCS3.1 file

sessionInfo( )
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
 [1] lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1       
 [4] dplyr_1.1.4          purrr_1.0.2          readr_2.1.5         
 [7] tidyr_1.3.1          tibble_3.2.1         ggplot2_3.4.4       
[10] tidyverse_2.0.0      flowWorkspace_4.14.2 CytoML_2.14.0       
[13] flowCore_2.14.1      optparse_1.7.4      

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          generics_0.1.3      tcltk_4.3.2        
 [4] stringi_1.8.3       lattice_0.22-5      hms_1.1.3          
 [7] magrittr_2.0.3      timechange_0.3.0    grid_4.3.2         
[10] RColorBrewer_1.1-3  ggcyto_1.30.0       plyr_1.8.9         
[13] jsonlite_1.8.8      graph_1.80.0        gridExtra_2.3      
[16] BiocManager_1.30.22 fansi_1.0.6         scales_1.3.0       
[19] XML_3.99-0.16.1     Rgraphviz_2.46.0    getopt_1.20.4      
[22] cli_3.6.2           rlang_1.1.3         RProtoBufLib_2.14.0
[25] Biobase_2.62.0      munsell_0.5.0       withr_3.0.0        
[28] yaml_2.3.8          cytolib_2.14.1      tools_4.3.2        
[31] ncdfFlow_2.48.0     tzdb_0.4.0          colorspace_2.1-0   
[34] BiocGenerics_0.48.1 vctrs_0.6.5         R6_2.5.1           
[37] matrixStats_1.2.0   stats4_4.3.2        lifecycle_1.0.4    
[40] zlibbioc_1.48.0     S4Vectors_0.40.2    RBGL_1.78.0        
[43] pkgconfig_2.0.3     pillar_1.9.0        hexbin_1.28.3      
[46] gtable_0.3.4        data.table_1.15.0   glue_1.7.0         
[49] Rcpp_1.0.12         tidyselect_1.2.0    compiler_4.3.2
flowWorkspace flowCore CytoML • 238 views
Entering edit mode

If your quesion is still unsolved, you should ask on the github of RGLab.

flowCore reads FCS 3.2, at least partially, as stated in the output, but I am unsure about CytoML or cytolib. Ask there.


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