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Known issues

Source: vignettes/known_issues.Rmd
known_issues.Rmd

This document lists known issues with the package and suggests possible solutions.

Issue: converted sce object has dimnames(), whilst the original anndata does not.

  • Affected backend: to_SCE
  • Affected slot(s): obsm, varm
  • Affected dtype(s): pca
  • Probable cause: convert
  • To investigate: TRUE
  • To fix: FALSE

Error message 

sampleFactors(reducedDims(sce)$pca) (`actual`) not equal to ad$obsm[["X_pca"]] (`expected`).
`dimnames(actual)` is a list `dimnames(expected)` is absent

Proposed solution

Investigate if this is a problem or not.

Session info 

## R version 4.5.1 (2025-06-13)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     desc_1.4.3        R6_2.6.1          fastmap_1.2.0    
##  [5] xfun_0.52         cachem_1.1.0      knitr_1.50        htmltools_0.5.8.1
##  [9] rmarkdown_2.29    lifecycle_1.0.4   cli_3.6.5         sass_0.4.10      
## [13] pkgdown_2.1.3     textshaping_1.0.1 jquerylib_0.1.4   systemfonts_1.2.3
## [17] compiler_4.5.1    tools_4.5.1       ragg_1.4.0        evaluate_1.0.4   
## [21] bslib_0.9.0       yaml_2.3.10       jsonlite_2.0.0    rlang_1.1.6      
## [25] fs_1.6.6          htmlwidgets_1.6.4