dviraran
commented
5 years ago Thanks!
Check out issue https://github.com/dviraran/SingleR/issues/74. Does this help?
Closed dioncst closed 5 years ago
dviraran
commented
5 years ago Thanks!
Check out issue https://github.com/dviraran/SingleR/issues/74. Does this help?
dioncst
commented
5 years ago Thanks!
Check out issue #74. Does this help?
Thanks! This work for me.
Hi! Thank your for your great package. But I came acorss a error recently when using CreateBigSingleRObject with a large integrated dataset of over 70,000 cells. Then I test the same thing in a small dataset, and still get this error. It seems that the temp singler objects have been created, but cannot be combined.
The error was:
"Error in singler$singler[[j]]$SingleR.single$labels[order, ] : subscript out of bounds"
My code was : " object_data = lung.combined@assays$RNA@data singler <- CreateBigSingleRObject(object_data, annot = NULL, project.name="lungcancer", N = 5000, technology = "10X", clusters = NULL, species = "Human", citation = "", ref.list = list(blueprint_encode), normalize.gene.length = F, variable.genes = "de", fine.tune = T, reduce.file.size = T, do.signatures = T, do.main.types = T, temp.dir = getwd(), numCores = 11) "
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
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
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] ggthemes_4.2.0 scales_1.0.0 ggplot2_3.2.1 tidyr_0.8.3 dplyr_0.8.3
[6] kableExtra_1.1.0 pheatmap_1.0.12 magrittr_1.5 Seurat_3.0.2 SingleR_1.0.0
loaded via a namespace (and not attached): [1] backports_1.1.4 plyr_1.8.4 igraph_1.2.4.1
[4] lazyeval_0.2.2 GSEABase_1.46.0 splines_3.6.1
[7] BiocParallel_1.18.1 listenv_0.7.0 GenomeInfoDb_1.20.0
[10] digest_0.6.20 foreach_1.4.7 htmltools_0.3.6
[13] gdata_2.18.0 memoise_1.1.0 cluster_2.1.0
[16] doParallel_1.0.15 ROCR_1.0-7 limma_3.40.6
[19] readr_1.3.1 globals_0.12.4 annotate_1.62.0
[22] doFuture_0.8.1 matrixStats_0.54.0 R.utils_2.9.0
[25] colorspace_1.4-1 rvest_0.3.4 blob_1.2.0
[28] ggrepel_0.8.1 xfun_0.8 crayon_1.3.4
[31] RCurl_1.95-4.12 jsonlite_1.6 graph_1.62.0
[34] zeallot_0.1.0 survival_2.43-3 zoo_1.8-6
[37] iterators_1.0.12 ape_5.3 glue_1.3.1
[40] gtable_0.3.0 zlibbioc_1.30.0 XVector_0.24.0
[43] webshot_0.5.1 DelayedArray_0.10.0 future.apply_1.3.0
[46] BiocGenerics_0.30.0 DBI_1.0.0 edgeR_3.26.6
[49] bibtex_0.4.2 Rcpp_1.0.2 metap_1.1
[52] viridisLite_0.3.0 xtable_1.8-4 reticulate_1.13
[55] bit_1.1-14 rsvd_1.0.2 SDMTools_1.1-221.1
[58] stats4_3.6.1 tsne_0.1-3 GSVA_1.32.0
[61] htmlwidgets_1.3 httr_1.4.1 gplots_3.0.1.1
[64] RColorBrewer_1.1-2 ica_1.0-2 pkgconfig_2.0.2
[67] XML_3.98-1.20 R.methodsS3_1.7.1 locfit_1.5-9.1
[70] tidyselect_0.2.5 rlang_0.4.0 reshape2_1.4.3
[73] later_0.8.0 AnnotationDbi_1.46.0 munsell_0.5.0
[76] pbmcapply_1.5.0 tools_3.6.1 RSQLite_2.1.2
[79] ggridges_0.5.1 evaluate_0.14 stringr_1.4.0
[82] npsurv_0.4-0 outliers_0.14 knitr_1.24
[85] bit64_0.9-7 fitdistrplus_1.0-14 caTools_1.17.1.2
[88] purrr_0.3.2 RANN_2.6.1 pbapply_1.4-1
[91] future_1.14.0 nlme_3.1-140 mime_0.7
[94] R.oo_1.22.0 xml2_1.2.2 compiler_3.6.1
[97] shinythemes_1.1.2 rstudioapi_0.10 plotly_4.9.0
[100] png_0.1-7 lsei_1.2-0 tibble_2.1.3
[103] geneplotter_1.62.0 stringi_1.4.3 lattice_0.20-38
[106] Matrix_1.2-17 vctrs_0.2.0 pillar_1.4.2
[109] Rdpack_0.11-0 lmtest_0.9-37 data.table_1.12.2
[112] cowplot_1.0.0 bitops_1.0-6 irlba_2.3.3
[115] gbRd_0.4-11 httpuv_1.5.1 GenomicRanges_1.36.0
[118] R6_2.4.0 promises_1.0.1 KernSmooth_2.23-15
[121] gridExtra_2.3 IRanges_2.18.1 codetools_0.2-16
[124] MASS_7.3-51.1 gtools_3.8.1 assertthat_0.2.1
[127] SummarizedExperiment_1.14.1 withr_2.1.2 sctransform_0.2.0
[130] S4Vectors_0.22.0 GenomeInfoDbData_1.2.1 hms_0.5.0
[133] parallel_3.6.1 grid_3.6.1 rmarkdown_1.14
[136] Rtsne_0.15 singscore_1.4.0 Biobase_2.44.0