Question: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
0
gravatar for kevin.rue
3 months ago by
kevin.rue220
University of Oxford
kevin.rue220 wrote:

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
ADD COMMENTlink modified 3 months ago by Aaron Lun24k • written 3 months ago by kevin.rue220
Answer: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
2
gravatar for Aaron Lun
3 months ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

This is because scater fails to use the implicit generic version of sweep, which apparently requires an explicit import from DelayedArray to get generic'd. This has now been fixed (1.13.4 and 1.12.2).

ADD COMMENTlink modified 3 months ago • written 3 months ago by Aaron Lun24k
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