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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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Replacement has x rows, data has y Error in Run.ProjecTILs #90

Closed whuangbinfo closed 3 months ago

whuangbinfo commented 3 months ago

I got the following error when trying to perform Run.ProjecTILs

Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in [<-.data.frame(*tmp*, , i, value = c(NA, NA, NA, NA, NA, : replacement has 17184 rows, data has 33255 6. stop(.error_bplist(res)) 5. .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO) 4. BiocParallel::bplapply(X = 1:length(query.list), BPPARAM = param, FUN = function(i) { projection.helper(query = query.list[[i]], ref = ref, filter.cells = filter.cells, query.assay = query.assay, ... 3. BiocParallel::bplapply(X = 1:length(query.list), BPPARAM = param, FUN = function(i) { projection.helper(query = query.list[[i]], ref = ref, filter.cells = filter.cells, query.assay = query.assay, ... 2. make.projection(query = query, ref = ref, filter.cells = filter.cells, ...) 1. Run.ProjecTILs(seurat_object, ref = ref_np, filter.cells = F, skip.normalize = T)

-- SESSIONINFO --

R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/Chicago tzcode source: internal

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

other attached packages: [1] GEOquery_2.70.0 Biobase_2.62.0 BiocGenerics_0.48.1 scGate_1.6.2 Matrix_1.6-5
[6] renv_1.0.7 umap_0.2.10.0 ProjecTILs_3.3.1 colorRamp2_0.1.0 ComplexHeatmap_2.18.0 [11] preprocessCore_1.64.0 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 future_1.33.2
[16] immunedeconv_2.1.0 EPIC_1.1.7 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[21] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[26] tidyverse_2.0.0 RColorBrewer_1.1-3 gridExtra_2.3 ggplot2_3.5.1 Seurat_5.1.0
[31] SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached): [1] matrixStats_1.3.0 spatstat.sparse_3.1-0 bitops_1.0-7 httr_1.4.7
[5] tools_4.4.1 sctransform_0.4.1 utf8_1.2.4 R6_2.5.1
[9] lazyeval_0.2.2 uwot_0.2.2 mMCPcounter_1.1.0 mgcv_1.9-1
[13] GetoptLong_1.0.5 withr_3.0.0 prettyunits_1.2.0 progressr_0.14.0
[17] textshaping_0.4.0 cli_3.6.3 spatstat.explore_3.2-7 fastDummies_1.7.3
[21] isoband_0.2.7 labeling_0.4.3 ComICS_1.0.4 spatstat.data_3.1-2
[25] genefilter_1.84.0 askpass_1.2.0 ggridges_0.5.6 pbapply_1.7-2
[29] systemfonts_1.1.0 R.utils_2.12.3 parallelly_1.37.1 limma_3.58.1
[33] readxl_1.4.3 rstudioapi_0.16.0 RSQLite_2.3.7 generics_0.1.3
[37] shape_1.4.6.1 testit_0.13 ica_1.0-3 spatstat.random_3.2-3
[41] fansi_1.0.6 S4Vectors_0.40.2 abind_1.4-5 R.methodsS3_1.8.2
[45] lifecycle_1.0.4 yaml_2.3.9 edgeR_4.0.16 SummarizedExperiment_1.32.0 [49] SparseArray_1.2.4 BiocFileCache_2.10.2 Rtsne_0.17 blob_1.2.4
[53] promises_1.3.0 crayon_1.5.3 miniUI_0.1.1.1 lattice_0.22-6
[57] cowplot_1.1.3 annotate_1.80.0 KEGGREST_1.42.0 pillar_1.9.0
[61] knitr_1.48 GenomicRanges_1.54.1 rjson_0.2.21 future.apply_1.11.2
[65] codetools_0.2-20 leiden_0.4.3.1 glue_1.7.0 remotes_2.5.0
[69] data.table_1.15.4 vctrs_0.6.5 png_0.1-8 spam_2.10-0
[73] cellranger_1.1.0 gtable_0.3.5 cachem_1.1.0 xfun_0.45
[77] S4Arrays_1.2.1 mime_0.12 pracma_2.4.4 survival_3.6-4
[81] SingleCellExperiment_1.24.0 pheatmap_1.0.12 statmod_1.5.0 fitdistrplus_1.1-11
[85] ROCR_1.0-11 nlme_3.1-164 bit64_4.0.5 progress_1.2.3
[89] filelock_1.0.3 RcppAnnoy_0.0.22 rprojroot_2.0.4 GenomeInfoDb_1.38.8
[93] data.tree_1.1.0 irlba_2.3.5.1 KernSmooth_2.23-24 STACAS_2.2.2
[97] colorspace_2.1-0 DBI_1.2.2 UCell_2.6.2 tidyselect_1.2.1
[101] bit_4.0.5 compiler_4.4.1 curl_5.2.1 httr2_1.0.1
[105] BiocNeighbors_1.20.2 xml2_1.3.6 DelayedArray_0.28.0 plotly_4.10.4
[109] scales_1.3.0 lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.36
[113] goftest_1.2-3 spatstat.utils_3.0-5 rmarkdown_2.27 XVector_0.42.0
[117] htmltools_0.5.8.1 pkgconfig_2.0.3 MatrixGenerics_1.14.0 dbplyr_2.5.0
[121] fastmap_1.2.0 rlang_1.1.3 GlobalOptions_0.1.2 htmlwidgets_1.6.4
[125] shiny_1.8.1.1 farver_2.1.2 zoo_1.8-12 jsonlite_1.8.8
[129] BiocParallel_1.36.0 R.oo_1.26.0 RCurl_1.98-1.16 magrittr_2.0.3
[133] GenomeInfoDbData_1.2.11 dotCall64_1.1-1 patchwork_1.2.0 munsell_0.5.1
[137] Rcpp_1.0.12 reticulate_1.38.0 stringi_1.8.4 zlibbioc_1.48.2
[141] MASS_7.3-60.0.1 plyr_1.8.9 listenv_0.9.1 ggrepel_0.9.5
[145] deldir_2.0-4 Biostrings_2.70.3 splines_4.4.1 tensor_1.5
[149] hms_1.1.3 circlize_0.4.16 locfit_1.5-9.10 igraph_2.0.3
[153] spatstat.geom_3.2-9 RcppHNSW_0.6.0 pkgload_1.4.0 reshape2_1.4.4
[157] biomaRt_2.59.1 stats4_4.4.1 XML_3.99-0.17 evaluate_0.24.0
[161] tzdb_0.4.0 httpuv_1.6.15 openssl_2.2.0 RANN_2.6.1
[165] polyclip_1.10-6 clue_0.3-65 scattermore_1.2 xtable_1.8-4
[169] RSpectra_0.16-1 later_1.3.2 ragg_1.3.2 viridisLite_0.4.2
[173] memoise_2.0.1 AnnotationDbi_1.64.1 IRanges_2.36.0 cluster_2.1.6
[177] timechange_0.3.0 sva_3.50.0 globals_0.16.3 here_1.0.1

mass-a commented 3 months ago

Hello Winston,

does your Seurat object have multiple layers? In that case, try running query <- JoinLayers(query) prior to Run.ProjecTILs() - does that work?

-m

whuangbinfo commented 3 months ago

Hello Winston,

does your Seurat object have multiple layers? In that case, try running query <- JoinLayers(query) prior to Run.ProjecTILs() - does that work?

-m

I solved the issue after converting the assays in my custom reference map to an earlier version. I think there is some version compatibility issue with the Seurat v5. Thanks!

Winston