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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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AggregateFlowFrames with channels given produces error #57

Open baj12 opened 1 year ago

baj12 commented 1 year ago

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 commented 1 year ago

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") ?