Entering edit mode
Hi,
Please see the reprex below.
This involves a few packages (scater, DelayedArray, BiocSingular), and I'm not exactly sure in which one the issue is taking place.
Any help is appreciated!
suppressPackageStartupMessages(library(TENxPBMCData))
tenx_pbmc3k <- TENxPBMCData(dataset="pbmc3k")
#> snapshotDate(): 2019-05-07
#> see ?TENxPBMCData and browseVignettes('TENxPBMCData') for documentation
#> downloading 0 resources
#> loading from cache
#> 'EH1607 : 1607'
suppressPackageStartupMessages(library(scater))
tenx_pbmc3k <- normalize(tenx_pbmc3k)
#> Warning in .local(object, ...): using library sizes as size factors
assayNames(tenx_pbmc3k)
#> [1] "counts" "logcounts"
assay(tenx_pbmc3k, "logcounts")
#> <32738 x 2700> DelayedMatrix object of type "double":
#> [,1] [,2] [,3] ... [,2699] [,2700]
#> ENSG00000243485 0 0 0 . 0 0
#> ENSG00000237613 0 0 0 . 0 0
#> ENSG00000186092 0 0 0 . 0 0
#> ENSG00000238009 0 0 0 . 0 0
#> ENSG00000239945 0 0 0 . 0 0
#> ... . . . . . .
#> ENSG00000215635 0 0 0 . 0 0
#> ENSG00000268590 0 0 0 . 0 0
#> ENSG00000251180 0 0 0 . 0 0
#> ENSG00000215616 0 0 0 . 0 0
#> ENSG00000215611 0 0 0 . 0 0
tenx_pbmc3k <- scater::runPCA(tenx_pbmc3k)
#> Error in .check_Ops_vector_arg_length(e, x_nrow, e_what = e_what, x_what = x_what): right object is longer than first dimension of left object
BiocManager::valid()
#> [1] TRUE
sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-apple-darwin18.5.0 (64-bit)
#> Running under: macOS Mojave 10.14.5
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
#>
#> attached base packages:
#> [1] parallel stats4 stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] scater_1.13.3 ggplot2_3.1.1
#> [3] TENxPBMCData_1.3.0 HDF5Array_1.13.1
#> [5] rhdf5_2.29.0 SingleCellExperiment_1.7.0
#> [7] SummarizedExperiment_1.15.1 DelayedArray_0.11.0
#> [9] BiocParallel_1.19.0 matrixStats_0.54.0
#> [11] Biobase_2.45.0 GenomicRanges_1.37.5
#> [13] GenomeInfoDb_1.21.1 IRanges_2.19.4
#> [15] S4Vectors_0.23.3 BiocGenerics_0.31.2
#>
#> loaded via a namespace (and not attached):
#> [1] viridis_0.5.1 httr_1.4.0
#> [3] BiocSingular_1.1.1 viridisLite_0.3.0
#> [5] bit64_0.9-7 AnnotationHub_2.17.3
#> [7] DelayedMatrixStats_1.7.0 shiny_1.3.2
#> [9] assertthat_0.2.1 interactiveDisplayBase_1.23.0
#> [11] BiocManager_1.30.4 highr_0.8
#> [13] BiocFileCache_1.9.0 blob_1.1.1
#> [15] vipor_0.4.5 GenomeInfoDbData_1.2.1
#> [17] yaml_2.2.0 pillar_1.4.0
#> [19] RSQLite_2.1.1 lattice_0.20-38
#> [21] glue_1.3.1 digest_0.6.19
#> [23] promises_1.0.1 XVector_0.25.0
#> [25] colorspace_1.4-1 htmltools_0.3.6
#> [27] httpuv_1.5.1 Matrix_1.2-17
#> [29] plyr_1.8.4 pkgconfig_2.0.2
#> [31] zlibbioc_1.31.0 purrr_0.3.2
#> [33] xtable_1.8-4 scales_1.0.0
#> [35] later_0.8.0 tibble_2.1.1
#> [37] withr_2.1.2 lazyeval_0.2.2
#> [39] magrittr_1.5 crayon_1.3.4
#> [41] mime_0.6 memoise_1.1.0
#> [43] evaluate_0.13 beeswarm_0.2.3
#> [45] tools_3.6.0 stringr_1.4.0
#> [47] Rhdf5lib_1.7.1 munsell_0.5.0
#> [49] irlba_2.3.3 AnnotationDbi_1.47.0
#> [51] compiler_3.6.0 rsvd_1.0.0
#> [53] rlang_0.3.4 grid_3.6.0
#> [55] RCurl_1.95-4.12 BiocNeighbors_1.3.1
#> [57] rappdirs_0.3.1 bitops_1.0-6
#> [59] rmarkdown_1.13 ExperimentHub_1.11.1
#> [61] gtable_0.3.0 DBI_1.0.0
#> [63] curl_3.3 R6_2.4.0
#> [65] gridExtra_2.3 knitr_1.23
#> [67] dplyr_0.8.1 bit_1.1-14
#> [69] ggbeeswarm_0.6.0 stringi_1.4.3
#> [71] Rcpp_1.0.1 dbplyr_1.4.0
#> [73] tidyselect_0.2.5 xfun_0.7
