AggregateFlowFrames with channels given produces error

[baj12]

I get an "Error: Subset out of bounds" error when using AggreateFlowFrames.

I got a reproducible example (see below) after debugging the cytoNorm examples...

> library(FlowSOM)
> fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
> f=flowCore::read.FCS(fileName)
> channels = unname(flowCore::parameters(f)@data[["name"]])[c(2,5,8,9,10)]
> ff_new <- AggregateFlowFrames(c(fileName, fileName), 1000,channels = channels)
Reading /Library/Frameworks/R.framework/Versions/4.2/Resources/library/FlowSOM/extdata/68983.fcs
Error: Subset out of bounds
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] FlowSOM_2.5.8 igraph_1.3.5 

loaded via a namespace (and not attached):
 [1] Biobase_2.56.0              httr_1.4.4                  tidyr_1.2.1                 jsonlite_1.8.1             
 [5] ConsensusClusterPlus_1.60.0 carData_3.0-5               RcppParallel_5.1.5          assertthat_0.2.1           
 [9] stats4_4.2.1                latticeExtra_0.6-30         RBGL_1.72.0                 flowWorkspace_4.9.1        
[13] yaml_2.3.5                  pillar_1.8.1                backports_1.4.1             lattice_0.20-45            
[17] glue_1.6.2                  digest_0.6.29               RColorBrewer_1.1-3          ggsignif_0.6.3             
[21] polyclip_1.10-0             colorspace_2.0-3            ggcyto_1.25.1               plyr_1.8.7                 
[25] ggnewscale_0.4.7            XML_3.99-0.10               pkgconfig_2.0.3             broom_1.0.1                
[29] zlibbioc_1.42.0             purrr_0.3.4                 flowCore_2.9.1              scales_1.2.1               
[33] tweenr_2.0.2                jpeg_0.1-9                  Rtsne_0.16                  ggforce_0.4.0              
[37] tibble_3.1.8                aws.s3_0.3.21               farver_2.1.1                generics_0.1.3             
[41] car_3.1-0                   ggplot2_3.3.6               ggpubr_0.4.0                withr_2.5.0                
[45] BiocGenerics_0.42.0         hexbin_1.28.2               cli_3.4.1                   magrittr_2.0.3             
[49] deldir_1.0-6                fansi_1.0.3                 MASS_7.3-58.1               rstatix_0.7.0              
[53] xml2_1.3.3                  graph_1.74.0                tools_4.2.1                 data.table_1.14.2          
[57] ncdfFlow_2.43.1             lifecycle_1.0.2             matrixStats_0.62.0          interp_1.1-3               
[61] S4Vectors_0.34.0            munsell_0.5.0               cluster_2.1.4               colorRamps_2.3.1           
[65] compiler_4.2.1              rlang_1.0.6                 grid_4.2.1                  rstudioapi_0.14            
[69] aws.signature_0.6.0         base64enc_0.1-3             cytolib_2.9.1               gtable_0.3.1               
[73] abind_1.4-5                 DBI_1.1.3                   curl_4.3.2                  R6_2.5.1                   
[77] RProtoBufLib_2.8.0          gridExtra_2.3               dplyr_1.0.10                utf8_1.2.2                 
[81] CytoML_2.8.1                Rgraphviz_2.40.0            Rcpp_1.0.9                  vctrs_0.4.2                
[85] png_0.1-7                   tidyselect_1.1.2           
> 

[SofieVG]

Hm, the example works for me without any issues, so it is probably something version related... Could you give it another try after updating the FlowSOM package with devtools::install_github("saeyslab/FlowSOM") ?