Error in crossprod(x, y) : requires numeric/complex matrix/vector arguments #375
Description
The milorR works well in the code below
seurat_milo <- Milo(as.SingleCellExperiment(seurat))%>%
buildGraph( k = 30, d = 50)%>%makeNhoods(prop = 0.2,k = 30,
d=50, refined = TRUE, refinement_scheme='graph')%>%
calcNhoodDistance(d=50)%>%
countCells(meta.data =seurat@meta.data,sample=sample)
but when I run seurat_milo<- buildNhoodGraph(seurat_milo) it reports
Error in crossprod(x, y) : requires numeric/complex matrix/vector arguments
the same error occurs in :
testNhoods(seurat_milo, design =as.formula(paste0('~ 0 + ',group)), design.df = design, model.contrasts = contrast.1,fdr.weighting="graph-overlap", norm.method="TMM")
(only occurs when I use 'graph-overlap' method to weigh fdr)
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] miloR_1.10.0 data.table_1.14.8 scales_1.4.0
[4] scater_1.28.0 scuttle_1.10.2 ggbeeswarm_0.7.2
[7] SeuratWrappers_0.3.19 SingleCellExperiment_1.22.0 SummarizedExperiment_1.28.0
[10] Biobase_2.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[13] IRanges_2.32.0 S4Vectors_0.36.2 BiocGenerics_0.46.0
[16] MatrixGenerics_1.12.3 matrixStats_1.0.0 edgeR_3.42.4
[19] limma_3.56.2 ggalluvial_0.12.5 ggrastr_1.0.2
[22] scattermore_1.2 tidydr_0.0.5 viridis_0.6.3
[25] viridisLite_0.4.2 lubridate_1.9.2 forcats_1.0.0
[28] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.2
[31] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[34] tidyverse_2.0.0 ggpubr_0.6.0 ggh4x_0.2.6
[37] ggplot2_3.5.2 Seurat_5.3.0 SeuratObject_5.2.0
[40] sp_2.0-0
loaded via a namespace (and not attached):
[1] fs_1.6.3 spatstat.sparse_3.0-1 bitops_1.0-7
[4] devtools_2.4.5 httr_1.4.5 RColorBrewer_1.1-3
[7] numDeriv_2016.8-1.1 profvis_0.3.8 tools_4.3.1
[10] sctransform_0.4.1 backports_1.4.1 utf8_1.2.3
[13] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[16] urlchecker_1.0.1 withr_2.5.0 prettyunits_1.1.1
[19] gridExtra_2.3 progressr_0.14.0 cli_3.6.1
[22] spatstat.explore_3.1-0 fastDummies_1.7.3 spatstat.data_3.0-1
[25] ggridges_0.5.7 pbapply_1.7-2 R.utils_2.12.2
[28] dichromat_2.0-0.1 sessioninfo_1.2.2 parallelly_1.36.0
[31] rstudioapi_0.15.0 generics_0.1.3 gtools_3.9.4
[34] ica_1.0-3 spatstat.random_3.1-4 car_3.1-2
[37] Matrix_1.6-5 fansi_1.0.4 abind_1.4-5
[40] R.methodsS3_1.8.2 lifecycle_1.0.3 carData_3.0-5
[43] SparseArray_1.2.4 Rtsne_0.16 promises_1.2.1
[46] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.21-8
[49] beachmat_2.16.0 cowplot_1.1.1 pillar_1.9.0
[52] future.apply_1.11.0 codetools_0.2-19 glue_1.6.2
[55] ggfun_0.0.9 remotes_2.5.0 vctrs_0.6.3
[58] png_0.1-8 spam_2.9-1 gtable_0.3.6
[61] cachem_1.0.8 S4Arrays_1.2.0 mime_0.12
[64] tidygraph_1.2.3 pracma_2.4.2 survival_3.5-7
[67] ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11
[70] nlme_3.1-163 usethis_2.2.2 RcppAnnoy_0.0.20
[73] rprojroot_2.0.3 irlba_2.3.5.1 vipor_0.4.5
[76] KernSmooth_2.23-22 colorspace_2.1-0 tidyselect_1.2.0
[79] processx_3.8.2 curl_5.0.1 compiler_4.3.1
[82] BiocNeighbors_1.18.0 desc_1.4.2 DelayedArray_0.28.0
[85] plotly_4.10.1 lmtest_0.9-40 callr_3.7.3
[88] digest_0.6.33 goftest_1.2-3 spatstat.utils_3.1-5
[91] XVector_0.38.0 htmltools_0.5.6 pkgconfig_2.0.3
[94] sparseMatrixStats_1.12.2 fastmap_1.1.1 rlang_1.1.1
[97] htmlwidgets_1.6.2 shiny_1.7.4 DelayedMatrixStats_1.22.6
[100] farver_2.1.1 zoo_1.8-12 jsonlite_1.8.7
[103] BiocParallel_1.32.6 R.oo_1.25.0 BiocSingular_1.16.0
[106] RCurl_1.98-1.12 magrittr_2.0.3 GenomeInfoDbData_1.2.9
[109] dotCall64_1.0-2 patchwork_1.3.2.9000 Rcpp_1.0.11
[112] reticulate_1.28 stringi_1.7.12 ggraph_2.1.0
[115] zlibbioc_1.44.0 MASS_7.3-60 plyr_1.8.8
[118] pkgbuild_1.4.2 parallel_4.3.1 listenv_0.9.0
[121] ggrepel_0.9.3 deldir_1.0-9 graphlayouts_0.8.4
[124] splines_4.3.1 tensor_1.5 hms_1.1.3
[127] locfit_1.5-9.8 ps_1.7.5 igraph_1.5.1
[130] spatstat.geom_3.1-0 ggsignif_0.6.4 RcppHNSW_0.4.1
[133] pkgload_1.3.2.1 reshape2_1.4.4 ScaledMatrix_1.8.1
[136] BiocManager_1.30.22 tzdb_0.4.0 tweenr_2.0.2
[139] httpuv_1.6.9 RANN_2.6.2 polyclip_1.10-4
[142] future_1.33.0 ggforce_0.4.1 rsvd_1.0.5
[145] broom_1.0.5 xtable_1.8-4 RSpectra_0.16-2
[148] rstatix_0.7.2 later_1.3.1 memoise_2.0.1
[151] beeswarm_0.4.0 cluster_2.1.4 timechange_0.2.0
[154] globals_0.16.2