Error in norm_cords$x - min(norm_cords$x) : non-numeric argument to binary operator

[krigia]

@YingMa0107 @YMalab
I would greatly appreciate your help with this error:

Run CARD deconvolution

CARD_obj = CARD_deconvolution(CARD_object = CARD_obj)

create reference matrix from scRNASeq...

Select Informative Genes! ...

Error in norm_cords$x - min(norm_cords$x) :
non-numeric argument to binary operator
In addition: Warning messages:
1: In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.0 GiB
2: In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB
3: In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.1 GiB

Thank you

[LuisAlonsoEsteban]

Same problem here, when trying to run CARD on the Mouse Cortex seqFISH+ dataset used in the paper. My sessionInfo() output is the following:

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.utf8 LC_CTYPE=Spanish_Spain.utf8 LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.utf8

time zone: Europe/Madrid
tzcode source: internal

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

other attached packages:
[1] wrMisc_1.14.1 MuSiC_1.0.0 TOAST_1.16.0 quadprog_1.5-8 limma_3.58.1 EpiDISH_2.18.0 ggplot2_3.5.1
[8] nnls_1.5 CARD_1.1 Biobase_2.62.0 BiocGenerics_0.48.1 Matrix_1.6-5

loaded via a namespace (and not attached):
[1] DBI_1.2.2 bitops_1.0-7 deldir_2.0-4 rlang_1.1.3 magrittr_2.0.3
[6] gridBase_0.4-7 spatstat.geom_3.2-9 matrixStats_1.2.0 e1071_1.7-14 compiler_4.3.3
[11] pbmcapply_1.5.1 vctrs_0.6.5 maps_3.4.2 reshape2_1.4.4 quantreg_5.97
[16] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.2 XVector_0.42.0 mcmc_0.9-8
[21] utf8_1.2.4 MatrixModels_0.5-3 purrr_1.0.2 zlibbioc_1.48.2 GenomeInfoDb_1.38.8
[26] DelayedArray_0.28.0 spatstat.utils_3.0-4 tweenr_2.0.3 parallel_4.3.3 cluster_2.1.6
[31] R6_2.5.1 spatstat.data_3.0-4 stringi_1.8.3 RColorBrewer_1.1-3 GGally_2.2.1
[36] GenomicRanges_1.54.1 Rcpp_1.0.12 SummarizedExperiment_1.32.0 iterators_1.0.14 fields_15.2
[41] IRanges_2.36.0 splines_4.3.3 tidyselect_1.2.1 rstudioapi_0.15.0 abind_1.4-5
[46] spatstat.random_3.2-3 doParallel_1.0.17 codetools_0.2-19 lattice_0.22-5 tibble_3.2.1
[51] plyr_1.8.9 withr_3.0.0 coda_0.19-4.1 survival_3.5-8 sf_1.0-15
[56] ggstats_0.5.1 scatterpie_0.2.1 units_0.8-5 proxy_0.4-27 polyclip_1.10-6
[61] pillar_1.9.0 MatrixGenerics_1.14.0 rngtools_1.5.2 KernSmooth_2.23-22 foreach_1.5.2
[66] stats4_4.3.3 ggfun_0.1.4 generics_0.1.3 sp_2.1-3 RCurl_1.98-1.14
[71] S4Vectors_0.40.2 munsell_0.5.1 scales_1.3.0 NMF_0.27 gtools_3.9.5
[76] class_7.3-22 glue_1.7.0 tools_4.3.3 SparseM_1.81 registry_0.5-1
[81] RcppML_0.3.7 RANN_2.6.1 dotCall64_1.1-1 grid_4.3.3 tidyr_1.3.1
[86] MCMCpack_1.7-0 colorspace_2.1-0 SingleCellExperiment_1.24.0 GenomeInfoDbData_1.2.11 ggforce_0.4.2
[91] cli_3.6.2 spam_2.10-0 fansi_1.0.6 S4Arrays_1.2.1 viridisLite_0.4.2
[96] dplyr_1.1.4 concaveman_1.1.0 corpcor_1.6.10 gtable_0.3.5 ggcorrplot_0.1.4.1
[101] digest_0.6.34 classInt_0.4-10 SparseArray_1.2.4 farver_2.1.1 lifecycle_1.0.4
[106] statmod_1.5.0 locfdr_1.1-8 MASS_7.3-60.0.1

Thanks in advanced.

[1JYL123]

I have the same error and I have solved it. I think the problem may be the data type of your spatial_location data frame is not integer. you can use as.integer() to make it become integer. This is how I solved my problem.