Error in prep.cytonorm

[mortadelo93]

Hi

I trying to use Spectre to integrate different flow samples. I have been following Discovery workflow with batch alignment using CytoNorm

Everything is okay until I run prep.cytonorm(). The next error turns out:

Step 1/4 - Splitting files for use with original FlowSOM function Step 2/4 - Running FlowSOM Reading sample1.fcs Error in if (sampleWithReplacement & (nrow(f) < cFile)) { : argument is of length zero

The command creates a folder with the fcs files but stacks there.

version R version 4.3.2 (2023-10-31)

package.version('Spectre') [1] "1.1.0"

Any idea?

Thank you

[markmelzer]

Hi @mortadelo93 ,

I encountered the same problem today and found this closed issue #169. As suggested, installing the development branch of Spectre solved this problem for me.

[mortadelo93]

Thanks @markmelzer. I will give it a try.

[tomashhurst]

Thanks @markmelzer ! @mortadelo93 if you still get stuck let us know.

[hrj21]

Hi folks, sorry to revive a dead issue but I'm having the same issue all of a sudden.

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8 
[2] LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/London
tzcode source: internal

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

other attached packages:
 [1] CytoNorm_2.0.2       FlowSOM_2.12.0       igraph_2.0.3        
 [4] flowViz_1.66.0       Biobase_2.62.0       BiocGenerics_0.48.1 
 [7] flowCore_2.14.2      class_7.3-22         caret_6.0-94        
[10] lattice_0.21-9       ggpubr_0.6.0         pheatmap_1.0.12     
[13] ggpointdensity_0.1.0 gridExtra_2.3        RColorBrewer_1.1-3  
[16] colorRamps_2.3.4     scales_1.3.0         ggthemes_5.1.0      
[19] ggplot2_3.5.1        reticulate_1.38.0    umap_0.2.10.0       
[22] Rtsne_0.17           rstudioapi_0.16.0    tidyr_1.3.1         
[25] dplyr_1.1.4          plyr_1.8.9           data.table_1.15.4   
[28] devtools_2.4.5       usethis_2.2.3        Spectre_1.1.0       

loaded via a namespace (and not attached):
  [1] jsonlite_1.8.8              magrittr_2.0.3             
  [3] farver_2.1.2                fs_1.6.4                   
  [5] vctrs_0.6.5                 memoise_2.0.1              
  [7] askpass_1.2.0               rstatix_0.7.2              
  [9] htmltools_0.5.8.1           curl_5.2.1                 
 [11] broom_1.0.6                 pROC_1.18.5                
 [13] parallelly_1.37.1           KernSmooth_2.23-22         
 [15] htmlwidgets_1.6.4           desc_1.4.3                 
 [17] lubridate_1.9.3             cachem_1.1.0               
 [19] mime_0.12                   lifecycle_1.0.4            
 [21] iterators_1.0.14            pkgconfig_2.0.3            
 [23] Matrix_1.6-5                R6_2.5.1                   
 [25] fastmap_1.2.0               future_1.33.2              
 [27] shiny_1.8.1.1               digest_0.6.36              
 [29] ggnewscale_0.4.10           colorspace_2.1-0           
 [31] S4Vectors_0.40.2            ps_1.7.6                   
 [33] RSpectra_0.16-1             pkgload_1.4.0              
 [35] labeling_0.4.3              cytolib_2.14.1             
 [37] fansi_1.0.6                 timechange_0.3.0           
 [39] polyclip_1.10-6             abind_1.4-5                
 [41] compiler_4.3.2              remotes_2.5.0              
 [43] withr_3.0.0                 ConsensusClusterPlus_1.66.0
 [45] backports_1.5.0             carData_3.0-5              
 [47] hexbin_1.28.3               pkgbuild_1.4.4             
 [49] ggforce_0.4.2               ggsignif_0.6.4             
 [51] MASS_7.3-60                 lava_1.8.0                 
 [53] openssl_2.2.0               sessioninfo_1.2.2          
 [55] ModelMetrics_1.2.2.2        tools_4.3.2                
 [57] httpuv_1.6.15               future.apply_1.11.2        
 [59] nnet_7.3-19                 glue_1.7.0                 
 [61] IDPmisc_1.1.21              callr_3.7.6                
 [63] nlme_3.1-163                promises_1.3.0             
 [65] grid_4.3.2                  cluster_2.1.4              
 [67] reshape2_1.4.4              generics_0.1.3             
 [69] recipes_1.0.10              gtable_0.3.5               
 [71] car_3.1-2                   utf8_1.2.4                 
 [73] foreach_1.5.2               pillar_1.9.0               
 [75] stringr_1.5.1               later_1.3.2                
 [77] splines_4.3.2               tweenr_2.0.3               
 [79] deldir_2.0-4                survival_3.5-7             
 [81] RProtoBufLib_2.14.1         tidyselect_1.2.1           
 [83] miniUI_0.1.1.1              stats4_4.3.2               
 [85] hardhat_1.4.0               timeDate_4032.109          
 [87] matrixStats_1.3.0           stringi_1.8.4              
 [89] codetools_0.2-19            interp_1.1-6               
 [91] tibble_3.2.1                cli_3.6.3                  
 [93] rpart_4.1.21                xtable_1.8-4               
 [95] munsell_0.5.1               processx_3.8.4             
 [97] Rcpp_1.0.12                 globals_0.16.3             
 [99] png_0.1-8                   XML_3.99-0.17              
[101] parallel_4.3.2              ellipsis_0.3.2             
[103] gower_1.0.1                 jpeg_0.1-10                
[105] latticeExtra_0.6-30         profvis_0.3.8              
[107] urlchecker_1.0.1            listenv_0.9.1              
[109] ipred_0.9-14                prodlim_2024.06.25         
[111] purrr_1.0.2                 rlang_1.1.4