runSCENIC_4_aucell_binarize error

[GreyRockIQ]

Hello
I have an error with runSCENIC_4_aucell_binarize function with mouse_ brain data example as below

Error in runSCENIC_4_aucell_binarize(scenicOptions) :
No cells passed the binarization.

Any suggestions to solve it?
Thanks
GreyRock

[jinlanzhan]

I encountered the same problem,and want to know how to solve it. Have you solved it yet，
Thank you, good luck

[jinlanzhan]

scenicOptions <- runSCENIC_4_aucell_binarize(scenicOptions)
Error in runSCENIC_4_aucell_binarize(scenicOptions) :
No cells passed the binarization.

Here is my sessionInfo()
sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

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

other attached packages:
[1] data.table_1.14.8 doParallel_1.0.17 iterators_1.0.14 BiocParallel_1.32.6 stringr_1.5.0
[6] loomR_0.2.1.9000 hdf5r_1.3.8 R6_2.5.1 SCENIC_1.3.1 SeuratObject_4.1.3
[11] Seurat_4.3.0.1 RcisTarget_1.18.2 GENIE3_1.20.0 AUCell_1.20.2 foreach_1.5.2

loaded via a namespace (and not attached):
[1] utf8_1.2.3 spatstat.explore_3.2-1 reticulate_1.30
[4] R.utils_2.12.2 tidyselect_1.2.0 RSQLite_2.3.1
[7] AnnotationDbi_1.60.2 htmlwidgets_1.6.2 grid_4.2.2
[10] Rtsne_0.16 devtools_2.4.5 munsell_0.5.0
[13] codetools_0.2-18 ica_1.0-3 DT_0.28
[16] future_1.33.0 miniUI_0.1.1.1 withr_2.5.0
[19] spatstat.random_3.1-5 colorspace_2.1-0 progressr_0.13.0
[22] Biobase_2.58.0 knitr_1.43 rstudioapi_0.14
[25] stats4_4.2.2 ROCR_1.0-11 tensor_1.5
[28] NMF_0.26 listenv_0.9.0 MatrixGenerics_1.10.0
[31] GenomeInfoDbData_1.2.9 polyclip_1.10-4 bit64_4.0.5
[34] rprojroot_2.0.3 parallelly_1.36.0 vctrs_0.6.1
[37] generics_0.1.3 xfun_0.39 GenomeInfoDb_1.34.9
[40] bitops_1.0-7 spatstat.utils_3.0-3 arrow_12.0.1
[43] cachem_1.0.6 DelayedArray_0.24.0 assertthat_0.2.1
[46] promises_1.2.0.1 scales_1.2.1 gtable_0.3.3
[49] globals_0.16.2 processx_3.8.1 goftest_1.2-3
[52] rlang_1.1.0 splines_4.2.2 lazyeval_0.2.2
[55] spatstat.geom_3.2-1 yaml_2.3.7 BiocManager_1.30.21
[58] reshape2_1.4.4 abind_1.4-5 crosstalk_1.2.0
[61] httpuv_1.6.11 tools_4.2.2 usethis_2.2.1
[64] gridBase_0.4-7 ggplot2_3.4.2 ellipsis_0.3.2
[67] jquerylib_0.1.4 RColorBrewer_1.1-3 BiocGenerics_0.44.0
[70] dynamicTreeCut_1.63-1 sessioninfo_1.2.2 ggridges_0.5.4
[73] Rcpp_1.0.10 plyr_1.8.8 sparseMatrixStats_1.10.0
[76] zlibbioc_1.44.0 purrr_1.0.1 RCurl_1.98-1.12
[79] ps_1.7.5 prettyunits_1.1.1 deldir_1.0-9
[82] pbapply_1.7-2 cowplot_1.1.1 urlchecker_1.0.1
[85] S4Vectors_0.36.2 zoo_1.8-12 SummarizedExperiment_1.28.0
[88] ggrepel_0.9.3 cluster_2.1.4 fs_1.6.2
[91] magrittr_2.0.3 scattermore_1.2 lmtest_0.9-40
[94] RANN_2.6.1 fitdistrplus_1.1-11 matrixStats_1.0.0
[97] pkgload_1.3.2 evaluate_0.21 patchwork_1.1.2
[100] mime_0.12 xtable_1.8-4 XML_3.99-0.14
[103] IRanges_2.32.0 gridExtra_2.3 compiler_4.2.2
[106] tibble_3.2.1 KernSmooth_2.23-20 crayon_1.5.2
[109] R.oo_1.25.0 htmltools_0.5.5 later_1.3.1
[112] tzdb_0.4.0 tidyr_1.3.0 DBI_1.1.3
[115] MASS_7.3-58.1 Matrix_1.5-3 cli_3.6.1
[118] R.methodsS3_1.8.2 igraph_1.5.0 GenomicRanges_1.50.2
[121] pkgconfig_2.0.3 registry_0.5-1 sp_2.0-0
[124] plotly_4.10.2 spatstat.sparse_3.0-2 annotate_1.76.0
[127] bslib_0.5.0 rngtools_1.5.2 XVector_0.38.0
[130] doRNG_1.8.6 callr_3.7.3 digest_0.6.31
[133] sctransform_0.3.5 RcppAnnoy_0.0.21 graph_1.76.0
[136] spatstat.data_3.0-1 Biostrings_2.66.0 rmarkdown_2.23
[139] leiden_0.4.3 uwot_0.1.16 DelayedMatrixStats_1.20.0
[142] GSEABase_1.60.0 curl_5.0.1 shiny_1.7.4
[145] lifecycle_1.0.3 nlme_3.1-160 jsonlite_1.8.7
[148] desc_1.4.2 viridisLite_0.4.2 fansi_1.0.4
[151] pillar_1.9.0 lattice_0.20-45 KEGGREST_1.38.0
[154] fastmap_1.1.0 httr_1.4.6 pkgbuild_1.4.2
[157] survival_3.4-0 glue_1.6.2 remotes_2.4.2
[160] png_0.1-8 bit_4.0.5 sass_0.4.6
[163] stringi_1.7.12 profvis_0.3.8 blob_1.2.4
[166] memoise_2.0.1 dplyr_1.1.2 irlba_2.3.5.1
[169] future.apply_1.11.0