spatialPerCellQC() 0 elements in value to replace 466401 elements

[ethanlewisbaird]

Hi, I am getting the following error and cannot understand why.

Error in [[<-(*tmp*, name, value = numeric(0)): 0 elements in value to replace 466401 elements
Traceback:

1. $<-(*tmp*, "CountArea", value = numeric(0))
2. $<-(*tmp*, "CountArea", value = numeric(0))
3. [[<-(*tmp*, name, value = numeric(0))
4. [[<-(*tmp*, name, value = numeric(0))
5. stop(paste(lv, "elements in value to replace", nrx, "elements"))
6. .handleSimpleError(function (cnd)
   . {
   . watcher$capture_plot_and_output()
   . cnd <- sanitize_call(cnd)
   . watcher$push(cnd)
   . switch(on_error, continue = invokeRestart("eval_continue"),
   . stop = invokeRestart("eval_stop"), error = NULL)
   . }, "0 elements in value to replace 466401 elements", base::quote([[<-(*tmp*,
   . name, value = numeric(0))))

[drighelli]

Hi thanks for reporting this!

Could you please provide a complete reproducible example (or the code snippet) leading to this error?

Also please provide your sessionInfo().

Thanks!

[ethanlewisbaird]

Thank you for your fast reply! Here is the code and sessionInfo

# Read Xenium SPE data
spe2 <- readXeniumSPE("/data/ebaird/spatial_omics/Dec25_xenium/outs")

# Exclude cells with NA AspectRatio caused by multi-polygons
cat("Excluding cells with NA AspectRatio caused by multi-polygons:\n")
na_cells <- which(is.na(colData(spe2)$AspectRatio))
if (length(na_cells) > 0) {
  spe2 <- spe2[, -na_cells]
  cat("Excluded", length(na_cells), "cells with NA AspectRatio.\n")
}

spe2 <- readAndAddPolygonsToSPE(spe2, boundariesType="csv")

spe2 <- spatialPerCellQC(spe2, use_altexps = FALSE, rmZeros=TRUE)

R version 4.5.2 (2025-10-31)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS/LAPACK: /data/ebaird/miniconda3/envs/xenium2/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Athens
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] SpaceTrooper_1.0.1 pheatmap_1.0.13
[3] pals_1.10 Banksy_1.6.0
[5] pbapply_1.7-4 sf_1.0-24
[7] data.table_1.18.2.1 org.Dm.eg.db_3.22.0
[9] AnnotationDbi_1.72.0 Seurat_5.4.0
[11] SeuratObject_5.3.0 sp_2.2-1
[13] SpatialExperimentIO_1.2.0 SpatialExperiment_1.20.0
[15] magick_2.9.0 DropletUtils_1.30.0
[17] BiocParallel_1.44.0 BayesSpace_1.20.2
[19] patchwork_1.3.2 SingleR_2.12.0
[21] scater_1.38.0 ggplot2_4.0.2
[23] igraph_2.1.4 scran_1.38.0
[25] scuttle_1.20.0 SingleCellExperiment_1.32.0
[27] SummarizedExperiment_1.40.0 Biobase_2.70.0
[29] GenomicRanges_1.62.1 Seqinfo_1.0.0
[31] IRanges_2.44.0 S4Vectors_0.48.0
[33] BiocGenerics_0.56.0 generics_0.1.4
[35] MatrixGenerics_1.22.0 matrixStats_1.5.0
[37] tidyr_1.3.2 dplyr_1.2.0

loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 dichromat_2.0-0.1
[3] DirichletReg_0.7-2 goftest_1.2-3
[5] Biostrings_2.78.0 HDF5Array_1.38.0
[7] vctrs_0.7.1 spatstat.random_3.4-4
[9] digest_0.6.39 png_0.1-8
[11] shape_1.4.6.1 proxy_0.4-29
[13] ggrepel_0.9.6 IRdisplay_1.1
[15] deldir_2.0-4 parallelly_1.46.1
[17] MASS_7.3-65 reshape2_1.4.5
[19] httpuv_1.6.16 foreach_1.5.2
[21] withr_3.0.2 ggpubr_0.6.2
[23] survival_3.8-6 memoise_2.0.1
[25] ggbeeswarm_0.7.3 systemfonts_1.3.1
[27] ragg_1.5.0 zoo_1.8-15
[29] IRkernel_1.3.2 R.oo_1.27.1
[31] DEoptimR_1.1-4 Formula_1.2-5
[33] KEGGREST_1.50.0 promises_1.5.0
[35] otel_0.2.0 httr_1.4.8
[37] rstatix_0.7.3 globals_0.19.0
[39] fitdistrplus_1.2-6 rhdf5filters_1.22.0
[41] rhdf5_2.54.1 units_1.0-0
[43] miniUI_0.1.2 base64enc_0.1-6
[45] curl_7.0.0 repr_1.1.7
[47] ScaledMatrix_1.18.0 h5mread_1.2.1
[49] polyclip_1.10-7 SparseArray_1.10.8
[51] xtable_1.8-4 stringr_1.6.0
[53] evaluate_1.0.5 S4Arrays_1.10.1
[55] BiocFileCache_3.0.0 glmnet_4.1-10
[57] irlba_2.3.7 colorspace_2.1-2
[59] filelock_1.0.3 ROCR_1.0-12
[61] reticulate_1.45.0 spatstat.data_3.1-9
[63] magrittr_2.0.4 lmtest_0.9-40
[65] later_1.4.6 viridis_0.6.5
[67] lattice_0.22-9 mapproj_1.2.12
[69] spatstat.geom_3.7-0 future.apply_1.20.1
[71] robustbase_0.99-7 scattermore_1.2
[73] cowplot_1.2.0 RcppAnnoy_0.0.23
[75] class_7.3-23 pillar_1.11.1
[77] nlme_3.1-168 iterators_1.0.14
[79] compiler_4.5.2 beachmat_2.26.0
[81] RSpectra_0.16-2 stringi_1.8.7
[83] tensor_1.5.1 plyr_1.8.9
[85] crayon_1.5.3 abind_1.4-8
[87] locfit_1.5-9.12 bit_4.6.0
[89] sandwich_3.1-1 codetools_0.2-20
[91] textshaping_1.0.4 BiocSingular_1.26.1
[93] e1071_1.7-17 plotly_4.12.0
[95] mime_0.13 splines_4.5.2
[97] Rcpp_1.1.1 fastDummies_1.7.5
[99] dbplyr_2.5.2 sparseMatrixStats_1.22.0
[101] maxLik_1.5-2.2 blob_1.3.0
[103] pbdZMQ_0.3-14 listenv_0.10.0
[105] DelayedMatrixStats_1.32.0 ggsignif_0.6.4
[107] RcppHungarian_0.3 tibble_3.3.1
[109] Matrix_1.7-4 statmod_1.5.1
[111] pkgconfig_2.0.3 tools_4.5.2
[113] cachem_1.1.0 aricode_1.0.3
[115] RSQLite_2.4.6 viridisLite_0.4.3
[117] DBI_1.2.3 fastmap_1.2.0
[119] scales_1.4.0 grid_4.5.2
[121] ica_1.0-3 broom_1.0.12
[123] coda_0.19-4.1 dotCall64_1.2
[125] carData_3.0-6 RANN_2.6.2
[127] farver_2.1.2 cli_3.6.5
[129] purrr_1.2.1 lifecycle_1.0.5
[131] dbscan_1.2.4 uwot_0.2.4
[133] arrow_22.0.0 bluster_1.20.0
[135] backports_1.5.0 gtable_0.3.6
[137] rjson_0.2.23 ggridges_0.5.7
[139] progressr_0.18.0 parallel_4.5.2
[141] limma_3.66.0 jsonlite_2.0.0
[143] edgeR_4.8.2 miscTools_0.6-30
[145] RcppHNSW_0.6.0 bitops_1.0-9
[147] bit64_4.6.0-1 assertthat_0.2.1
[149] xgboost_3.2.0.1 Rtsne_0.17
[151] spatstat.utils_3.2-1 BiocNeighbors_2.4.0
[153] metapod_1.18.0 dqrng_0.3.2
[155] spatstat.univar_3.1-6 R.utils_2.13.0
[157] lazyeval_0.2.2 shiny_1.12.1
[159] htmltools_0.5.9 sctransform_0.4.3
[161] rappdirs_0.3.4 glue_1.8.0
[163] spam_2.11-3 httr2_1.2.2
[165] XVector_0.50.0 RCurl_1.98-1.17
[167] microbenchmark_1.5.0 mclust_6.1.2
[169] classInt_0.4-11 gridExtra_2.3
[171] sccore_1.0.6 R6_2.6.1
[173] labeling_0.4.3 cluster_2.1.8.2
[175] Rhdf5lib_1.32.0 DelayedArray_0.36.0
[177] tidyselect_1.2.1 vipor_0.4.7
[179] maps_3.4.3 car_3.1-5
[181] sfheaders_0.4.5 future_1.69.0
[183] leidenAlg_1.1.5 rsvd_1.0.5
[185] KernSmooth_2.23-26 S7_0.2.1
[187] htmlwidgets_1.6.4 RColorBrewer_1.1-3
[189] rlang_1.1.7 spatstat.sparse_3.1-0
[191] spatstat.explore_3.7-0 uuid_1.2-2
[193] Cairo_1.7-0 beeswarm_0.4.0

[drighelli]

Do you mind to show the counts(spe2) and the names(colData(spe2))?

I would also suggest to install the latest devel version of the package with BiocManager::install("SpaceTrooper", version="devel")

[ethanlewisbaird]

6 x 466401 sparse Matrix of class "dgCMatrix"

5-HT1A . . 1 . . . 1 . . . 1 . . . . . . . . . . . . . . . . . . . . . . .
5-HT1B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5-HT2A . . . . . 1 . . . . . . . . . . . 1 . . . . . . . . . 1 . . . . . .
5-HT2B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5-HT7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7B2 . . . . . . . . . 2 . . 1 . . . . . . . . . . . . . . . . . . . . .

'cell_id''transcript_counts''control_probe_counts''genomic_control_counts''control_codeword_counts''unassigned_codeword_counts''deprecated_codeword_counts''total_counts''nucleus_area''nucleus_count''segmentation_method''sample_id''AspectRatio''Area_um''polygons''sum''detected''total'