Error while running liver_analysis.Rmd

[rghosh670]

I was running liver_analysis.Rmd, when I hit this error:

Were there any other files I needed to download prior to running the script, or are any of my packages outdated?

 > sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] scater_1.16.2               ggplot2_3.3.2               SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2
 [5] DelayedArray_0.14.1         matrixStats_0.56.0          Biobase_2.48.0              GenomicRanges_1.40.0       
 [9] GenomeInfoDb_1.24.2         IRanges_2.22.2              S4Vectors_0.26.1            BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6              fs_1.5.0                  usethis_1.6.1             devtools_2.3.1            bit64_4.0.5              
 [6] RColorBrewer_1.1-2        rprojroot_1.3-2           tools_4.0.2               backports_1.1.10          R6_2.4.1                 
[11] irlba_2.3.3               vipor_0.4.5               DBI_1.1.0                 colorspace_1.4-1          withr_2.2.0              
[16] gridExtra_2.3             tidyselect_1.1.0          prettyunits_1.1.1         processx_3.4.4            bit_4.0.4                
[21] compiler_4.0.2            cli_2.0.2                 BiocNeighbors_1.6.0       desc_1.2.0                scales_1.1.1             
[26] callr_3.4.4               stringr_1.4.0             digest_0.6.25             rmarkdown_2.3             XVector_0.28.0           
[31] pkgconfig_2.0.3           htmltools_0.5.0           sessioninfo_1.1.1         rlang_0.4.7               rstudioapi_0.11          
[36] RSQLite_2.2.0             DelayedMatrixStats_1.10.1 generics_0.0.2            BiocParallel_1.22.0       gtools_3.8.2             
[41] dplyr_1.0.2               RCurl_1.98-1.2            magrittr_1.5              BiocSingular_1.4.0        GenomeInfoDbData_1.2.3   
[46] patchwork_1.0.1           Matrix_1.2-18             Rcpp_1.0.5                ggbeeswarm_0.6.0          munsell_0.5.0            
[51] fansi_0.4.1               viridis_0.5.1             lifecycle_0.2.0           stringi_1.5.3             yaml_2.2.1               
[56] zlibbioc_1.34.0           pkgbuild_1.1.0            plyr_1.8.6                grid_4.0.2                blob_1.2.1               
[61] crayon_1.3.4              lattice_0.20-41           knitr_1.29                ps_1.3.4                  pillar_1.4.6             
[66] pkgload_1.1.0             glue_1.4.2                evaluate_0.14             BiocManager_1.30.10       remotes_2.2.0            
[71] vctrs_0.3.4               testthat_2.3.2            gtable_0.3.0              purrr_0.3.4               reshape_0.8.8            
[76] assertthat_0.2.1          xfun_0.17                 rsvd_1.0.3                DCARS_0.3.5               viridisLite_0.3.0        
[81] tibble_3.0.3              beeswarm_0.2.3            tinytex_0.25              AnnotationDbi_1.50.3      memoise_1.1.0            
[86] ellipsis_0.3.1 

[shazanfar]

Hi @rghosh670, thanks for your message. It looks like the issue is that the default assay slot "logcounts" is not found for calculateTSNE. I've updated the script with an argument to extract from the correct assay slot "scMerge". Hope that helps! Cheers, Shila