scran ScoreMarkers throws a warning
1
0
Entering edit mode
Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 7 weeks ago
Germany

When running the command scoreMarkers in R 4.3 The function throws this error I don't figure as this parameter doesn't exist in the function.

library(scran)
marker.info <- scoreMarkers(sce, colLabels(sce), full.stats=TRUE)

and the warning is multiple times this:

Warning: useNames = NA is deprecated. Instead, specify either useNames = TRUE or useNames = TRUE.

It doesn't even make sense.

I know it is not so worrisome, but it is annoying.

any ideas what it means?

thanks

Assa

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] EnhancedVolcano_1.18.0      limma_3.56.2                ggraph_2.1.0                patchwork_1.1.2            
 [5] PCAtools_2.12.0             ensembldb_2.24.0            AnnotationFilter_1.24.0     GenomicFeatures_1.52.0     
 [9] gridExtra_2.3               ggrepel_0.9.3               scran_1.28.1                scater_1.28.0              
[13] scuttle_1.10.1              AnnotationDbi_1.62.1        AnnotationHub_3.8.0         BiocFileCache_2.8.0        
[17] dbplyr_2.3.2                SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 Biobase_2.60.0             
[21] GenomicRanges_1.52.0        GenomeInfoDb_1.36.0         IRanges_2.34.0              S4Vectors_0.38.1           
[25] BiocGenerics_0.46.0         MatrixGenerics_1.12.0       matrixStats_1.0.0           lubridate_1.9.2            
[29] forcats_1.0.0               stringr_1.5.0               dplyr_1.1.2                 purrr_1.0.1                
[33] readr_2.1.4                 tidyr_1.3.0                 tibble_3.2.1                ggplot2_3.4.2              
[37] tidyverse_2.0.0             SeuratObject_4.1.3          Seurat_4.3.0               

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.32.0           spatstat.sparse_3.0-1         bitops_1.0-7                  httr_1.4.6                   
  [5] RColorBrewer_1.1-3            backports_1.4.1               tools_4.3.0                   sctransform_0.3.5            
  [9] utf8_1.2.3                    R6_2.5.1                      lazyeval_0.2.2                uwot_0.1.14                  
 [13] withr_2.5.0                   sp_1.6-1                      prettyunits_1.1.1             progressr_0.13.0             
 [17] textshaping_0.3.6             cli_3.6.1                     spatstat.explore_3.2-1        labeling_0.4.2               
 [21] spatstat.data_3.0-1           ggridges_0.5.4                pbapply_1.7-0                 systemfonts_1.0.4            
 [25] Rsamtools_2.16.0              parallelly_1.36.0             rstudioapi_0.14               RSQLite_2.3.1                
 [29] FNN_1.1.3.2                   generics_0.1.3                BiocIO_1.10.0                 ica_1.0-3                    
 [33] spatstat.random_3.1-5         Matrix_1.5-4.1                ggbeeswarm_0.7.2              fansi_1.0.4                  
 [37] abind_1.4-5                   lifecycle_1.0.3               yaml_2.3.7                    edgeR_3.42.4                 
 [41] Rtsne_0.16                    grid_4.3.0                    blob_1.2.4                    promises_1.2.0.1             
 [45] dqrng_0.3.0                   crayon_1.5.2                  miniUI_0.1.1.1                lattice_0.21-8               
 [49] beachmat_2.16.0               cowplot_1.1.1                 KEGGREST_1.40.0               pillar_1.9.0                 
 [53] knitr_1.43                    metapod_1.8.0                 rjson_0.2.21                  future.apply_1.11.0          
 [57] codetools_0.2-19              leiden_0.4.3                  glue_1.6.2                    data.table_1.14.8            
 [61] vctrs_0.6.3                   png_0.1-8                     gtable_0.3.3                  cachem_1.0.8                 
 [65] xfun_0.39                     S4Arrays_1.0.4                mime_0.12                     tidygraph_1.2.3              
 [69] survival_3.5-5                statmod_1.5.0                 bluster_1.10.0                interactiveDisplayBase_1.38.0
 [73] ellipsis_0.3.2                fitdistrplus_1.1-11           ROCR_1.0-11                   nlme_3.1-162                 
 [77] bit64_4.0.5                   progress_1.2.2                filelock_1.0.2                RcppAnnoy_0.0.20             
 [81] irlba_2.3.5.1                 vipor_0.4.5                   KernSmooth_2.23-21            colorspace_2.1-0             
 [85] DBI_1.1.3                     tidyselect_1.2.0              bit_4.0.5                     compiler_4.3.0               
 [89] curl_5.0.1                    BiocNeighbors_1.18.0          xml2_1.3.4                    DelayedArray_0.26.3          
 [93] plotly_4.10.2                 rtracklayer_1.60.0            checkmate_2.2.0               scales_1.2.1                 
 [97] lmtest_0.9-40                 rappdirs_0.3.3                digest_0.6.31                 goftest_1.2-3                
[101] spatstat.utils_3.0-3          rmarkdown_2.22                XVector_0.40.0                htmltools_0.5.5              
[105] pkgconfig_2.0.3               sparseMatrixStats_1.12.0      fastmap_1.1.1                 rlang_1.1.1                  
[109] htmlwidgets_1.6.2             shiny_1.7.4                   DelayedMatrixStats_1.22.0     farver_2.1.1                 
[113] zoo_1.8-12                    jsonlite_1.8.5                BiocParallel_1.34.2           BiocSingular_1.16.0          
[117] RCurl_1.98-1.12               magrittr_2.0.3                GenomeInfoDbData_1.2.10       munsell_0.5.0                
[121] Rcpp_1.0.10                   viridis_0.6.3                 reticulate_1.29               stringi_1.7.12               
[125] zlibbioc_1.46.0               MASS_7.3-60                   plyr_1.8.8                    parallel_4.3.0               
[129] listenv_0.9.0                 deldir_1.0-9                  graphlayouts_1.0.0            Biostrings_2.68.1            
[133] splines_4.3.0                 tensor_1.5                    hms_1.1.3                     locfit_1.5-9.7               
[137] clustree_0.5.0                igraph_1.4.3                  spatstat.geom_3.2-1           reshape2_1.4.4               
[141] biomaRt_2.56.0                ScaledMatrix_1.8.1            BiocVersion_3.17.1            XML_3.99-0.14                
[145] evaluate_0.21                 BiocManager_1.30.20           tweenr_2.0.2                  tzdb_0.4.0                   
[149] httpuv_1.6.11                 RANN_2.6.1                    polyclip_1.10-4               future_1.32.0                
[153] scattermore_1.1               ggforce_0.4.1                 rsvd_1.0.5                    xtable_1.8-4                 
[157] restfulr_0.0.15               later_1.3.1                   ragg_1.2.5                    viridisLite_0.4.2            
[161] memoise_2.0.1                 beeswarm_0.4.0                GenomicAlignments_1.36.0      cluster_2.1.4                
[165] timechange_0.2.0              globals_0.16.2
scoreMarkers scran • 9.9k views
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2
Entering edit mode
ATpoint ★ 4.6k
@atpoint-13662
Last seen 7 hours ago
Germany

My guess with the help of googleing this:

Taken together, any of the matrixStats-fu that is happening inside of this scran function uses some sort of not-super-recent code/command, likely not even something that the dev actively puts (or not), or it is DelayedMatrixStats that internally still uses this slightly outdated command/code -- that triggers this warning (not error)

So either ignore, try to update every relevant package (DelayedMatrixStats would be the first go-to), or put suppressWarnings(). If you google this error you see that this warning pops up in vignettes and Rmarkdowns of many packages, so it's a general boilerplatish thing, and not specific to scran.
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0
Entering edit mode

@atpoint's explanation of the issue is correct (I'm the developer of DelayedMatrixStats).

If you upgrade DelayedMatrixStats and MatrixGenerics to their latest versions (basically just run BiocManager::install() to update all your packages) this warning should go away. This is what I see with an up-to-date installation of Bioconductor 3.17.

suppressPackageStartupMessages(library(scran))

# Example adapted from ?scran::scoreMarkers
suppressPackageStartupMessages(library(scuttle))
sce <- mockSCE()
sce <- logNormCounts(sce)
# Any clustering method is okay, only using k-means for convenience.
kout <- kmeans(t(logcounts(sce)), centers=4) 
out <- scoreMarkers(sce, groups=kout$cluster, full.stats=TRUE)

BiocManager::valid()
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com/
#> [1] TRUE

sessionInfo()
#> R version 4.3.0 (2023-04-21)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#> 
#> Matrix products: default
#> BLAS:   /stornext/System/data/apps/R/R-4.3.0/lib64/R/lib/libRblas.so 
#> LAPACK: /stornext/System/data/apps/R/R-4.3.0/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Australia/Melbourne
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] scran_1.28.1                scuttle_1.10.1             
#>  [3] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
#>  [5] Biobase_2.60.0              GenomicRanges_1.52.0       
#>  [7] GenomeInfoDb_1.36.0         IRanges_2.34.0             
#>  [9] S4Vectors_0.38.1            BiocGenerics_0.46.0        
#> [11] MatrixGenerics_1.12.2       matrixStats_1.0.0          
#> 
#> loaded via a namespace (and not attached):
#>  [1] dqrng_0.3.0               bitops_1.0-7             
#>  [3] lattice_0.21-8            magrittr_2.0.3           
#>  [5] digest_0.6.31             evaluate_0.21            
#>  [7] sparseMatrixStats_1.12.0  grid_4.3.0               
#>  [9] fastmap_1.1.1             Matrix_1.5-4             
#> [11] limma_3.56.2              BiocManager_1.30.21      
#> [13] codetools_0.2-19          cli_3.6.1                
#> [15] rlang_1.1.1               crayon_1.5.2             
#> [17] XVector_0.40.0            BiocNeighbors_1.18.0     
#> [19] reprex_2.0.2              withr_2.5.0              
#> [21] DelayedArray_0.26.3       yaml_2.3.7               
#> [23] metapod_1.8.0             S4Arrays_1.0.4           
#> [25] tools_4.3.0               beachmat_2.16.0          
#> [27] parallel_4.3.0            BiocParallel_1.34.2      
#> [29] locfit_1.5-9.8            GenomeInfoDbData_1.2.10  
#> [31] rsvd_1.0.5                lifecycle_1.0.3          
#> [33] zlibbioc_1.46.0           edgeR_3.42.4             
#> [35] BiocSingular_1.16.0       fs_1.6.2                 
#> [37] bluster_1.10.0            cluster_2.1.4            
#> [39] irlba_2.3.5.1             pkgconfig_2.0.3          
#> [41] ScaledMatrix_1.8.1        glue_1.6.2               
#> [43] Rcpp_1.0.10               statmod_1.5.0            
#> [45] xfun_0.39                 rstudioapi_0.14          
#> [47] knitr_1.43                igraph_1.5.0             
#> [49] htmltools_0.5.5           rmarkdown_2.22           
#> [51] DelayedMatrixStats_1.22.1 compiler_4.3.0           
#> [53] RCurl_1.98-1.12
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