error in prep.cytonorm

[domivf]

Dear developers, I am running into a problem while executing the prep.cytonorm function.

When I run the function, looking like that cytnrm <- prep.cytonorm(dat = ref.dat, cellular.cols = cellular.cols, cluster.cols = cluster.cols, batch.col = batch.col, sample.col = sample.col, meta.k = 15) I get always this error message in the console

Step 1/3. Mapping data Step 2/3. Merging data Step 3/3. Returning data Step 1/4 - Splitting files for use with original FlowSOM function Step 2/4 - Running FlowSOM Error in if (nrow(fsom$data) != nrow(dat)) { : argument is of length zero

if I run the same script on my mac (Spectre Version 0.4.2), it runs through, so I am not sure if it's a Windows problem or the newer Spectre version.

R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale: [1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252 LC_MONETARY=English_Germany.1252 LC_NUMERIC=C LC_TIME=English_Germany.1252

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

other attached packages: [1] igraph_1.3.0 CytoNorm_0.0.7 flowViz_1.54.0 Biobase_2.50.0 BiocGenerics_0.36.1 flowCore_2.2.0 class_7.3-17 caret_6.0-92 lattice_0.20-41
[10] ggpubr_0.4.0 pheatmap_1.0.12 gridExtra_2.3 colorRamps_2.3.1 scales_1.2.0 ggthemes_4.2.4 reticulate_1.24 umap_0.2.8.0 Rtsne_0.16
[19] rstudioapi_0.13 plyr_1.8.7 data.table_1.14.2 MetBrewer_0.2.0 factoextra_1.0.7 ggpointdensity_0.1.0 RColorBrewer_1.1-3 gghighlight_0.3.2 forcats_0.5.1
[28] stringr_1.4.0 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7 tidyverse_1.3.1 magrittr_2.0.3 ggrepel_0.9.1 dplyr_1.0.9
[37] ggplot2_3.3.6 pals_1.7 Spectre_1.0.0 devtools_2.4.3 usethis_2.1.5

loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.2 grid_4.0.2 pROC_1.18.0 aws.signature_0.6.0 munsell_0.5.0
[7] codetools_0.2-16 future_1.25.0 withr_2.5.0 colorspace_2.0-3 stats4_4.0.2 ggsignif_0.6.3
[13] listenv_0.8.0 flowWorkspace_4.2.0 rprojroot_2.0.3 parallelly_1.31.1 vctrs_0.4.1 generics_0.1.2
[19] ipred_0.9-12 R6_2.5.1 cachem_1.0.6 assertthat_0.2.1 nnet_7.3-14 gtable_0.3.0
[25] globals_0.15.0 processx_3.5.3 RProtoBufLib_2.2.0 timeDate_3043.102 rlang_1.0.2 splines_4.0.2
[31] rstatix_0.7.0 ModelMetrics_1.2.2.2 dichromat_2.0-0.1 hexbin_1.28.2 broom_0.8.0 yaml_2.3.5
[37] reshape2_1.4.4 abind_1.4-5 modelr_0.1.8 backports_1.4.1 IDPmisc_1.1.20 RBGL_1.66.0
[43] tools_4.0.2 lava_1.6.10 ellipsis_0.3.2 sessioninfo_1.2.2 Rcpp_1.0.8.3 base64enc_0.1-3
[49] zlibbioc_1.36.0 ps_1.7.0 FlowSOM_1.22.0 prettyunits_1.1.1 rpart_4.1-15 openssl_2.0.0
[55] S4Vectors_0.28.1 haven_2.5.0 cluster_2.1.0 fs_1.5.2 ncdfFlow_2.36.0 RSpectra_0.16-1
[61] reprex_2.0.1 matrixStats_0.62.0 pkgload_1.2.4 hms_1.1.1 XML_3.99-0.9 jpeg_0.1-9
[67] readxl_1.4.0 ggcyto_1.18.0 testthat_3.1.4 compiler_4.0.2 maps_3.4.0 KernSmooth_2.23-17
[73] crayon_1.5.1 tzdb_0.3.0 RcppParallel_5.1.5 lubridate_1.8.0 aws.s3_0.3.21 DBI_1.1.2
[79] dbplyr_2.1.1 MASS_7.3-51.6 Matrix_1.2-18 car_3.0-13 brio_1.1.3 cli_3.3.0
[85] gower_1.0.0 pkgconfig_2.0.3 recipes_0.2.0 xml2_1.3.3 foreach_1.5.2 hardhat_0.2.0
[91] prodlim_2019.11.13 rvest_1.0.2 callr_3.7.0 digest_0.6.29 tsne_0.1-3.1 ConsensusClusterPlus_1.54.0 [97] graph_1.68.0 cellranger_1.1.0 curl_4.3.2 lifecycle_1.0.1 nlme_3.1-148 jsonlite_1.8.0
[103] carData_3.0-5 mapproj_1.2.8 desc_1.4.1 askpass_1.1 fansi_1.0.3 pillar_1.7.0
[109] fastmap_1.1.0 httr_1.4.3 pkgbuild_1.3.1 survival_3.1-12 glue_1.6.2 remotes_2.4.2
[115] png_0.1-7 iterators_1.0.14 Rgraphviz_2.34.0 stringi_1.7.6 CytoML_2.2.2 latticeExtra_0.6-29
[121] memoise_2.0.1 cytolib_2.2.1 future.apply_1.9.0

[tomashhurst]

Hi @domivf in this case it might be the version of FlowSOM -- there was an update a little while ago that changed the FlowSOM object structure that was causing some issues. What version of FlowSOM are you using?

[domivf]

Dear @tomashhurst, currently FlowSOM version 1.22.0 is installed, as you can see in the attached pic

Best

Domi

[domivf]

Dear @tomashhurst installing FlowSOM from github again resolved the issue :) Thanks for pointing out that FlowSOM could be the issue here.

[tomashhurst]

No problem! Let us know if any other issues come up.