decontX (celda package)
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Shea • 0
Last seen 22 days ago
United States

I am trying to run the decontX function (celda package) to perform ambient RNA correction on my scRNAseq dataset. I'm using code that was written by another person previously, so I know that it should work. the session info for when the code was originally run successfully by the other person is not available to me.

What I've tried/Extra info.

  1. made sure irlba and Matrix are installed and loaded, I re-installed them thinking that updating them would make them work.
  2. I had a lot of trouble installing celda, and had to individually install many of its dependencies--which were revealed to me in error messages when I attempted the installation. The person who originally wrote the code did not explicitly load in any of these dependencies, which makes me think the fact that I needed to install and these dependencies was not a problem that she also had. Many of them are no longer available on cran, so I had to go to the cran archives and download the earliest version I could find. These dependent packages include assertive.base, assertive.files, assertive.numbers,, assertive.types, gridGraphics. It is possible that there is something wrong with one of these that is causing the code not to work--ie maybe one of the versions I installed does not play well with Matrix or irlba.

I am running

sce <- decontX(sce, seed = 12345)

My output message is.

Starting DecontX

Thu Nov 9 15:11:36 2023 .. Analyzing all cells Thu Nov 9 15:11:36 2023 .... Converting to sparse matrix Thu Nov 9 15:11:37 2023 .... Generating UMAP and estimating cell types Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : function 'as_cholmod_sparse' not provided by package 'Matrix'

sessionInfo( )

```R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/ LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/


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

other attached packages: [1] celda_1.12.0 scDblFinder_1.10.0 readxl_1.4.0 gridExtra_2.3
[5] cowplot_1.1.1 ComplexHeatmap_2.12.1 scales_1.2.1 scran_1.24.1
[9] Matrix_1.6-2 readr_2.1.2 scds_1.12.0 scater_1.24.0
[13] ggplot2_3.4.4 scuttle_1.6.3 DropletUtils_1.16.0 SingleCellExperiment_1.18.1 [17] SummarizedExperiment_1.26.1 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[21] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[25] matrixStats_1.1.0

loaded via a namespace (and not attached): [1] circlize_0.4.15 RcppEigen_0. plyr_1.8.9 igraph_1.5.1
[5] assertive.files_0.0-2 enrichR_3.2 multipanelfigure_2.1.2 BiocParallel_1.30.4
[9] digest_0.6.33 foreach_1.5.2 magick_2.8.1 viridis_0.6.4
[13] fansi_1.0.3 magrittr_2.0.3 assertive.numbers_0.0-2 ScaledMatrix_1.4.1
[17] cluster_2.1.3 doParallel_1.0.17 tzdb_0.3.0 limma_3.52.4
[21] Biostrings_2.64.0 R.utils_2.12.2 colorspace_2.0-3 ggrepel_0.9.4
[25] WriteXLS_6.4.0 dplyr_1.1.3 crayon_1.5.1 RCurl_1.98-1.6
[29] jsonlite_1.8.7 iterators_1.0.14 glue_1.6.2 gtable_0.3.0
[33] zlibbioc_1.42.0 XVector_0.36.0 GetoptLong_1.0.5 DelayedArray_0.22.0
[37] BiocSingular_1.12.0 Rhdf5lib_1.18.2 shape_1.4.6 HDF5Array_1.24.2
[41] edgeR_3.38.4 Rcpp_1.0.8.3 viridisLite_0.4.0 clue_0.3-65
[45] gridGraphics_0.5-1 dqrng_0.3.1 rsvd_1.0.5 metapod_1.4.0
[49] httr_1.4.3 RColorBrewer_1.1-3 ellipsis_0.3.2 pkgconfig_2.0.3
[53] XML_3.99-0.15 R.methodsS3_1.8.2 uwot_0.1.16 locfit_1.5-9.8
[57] utf8_1.2.2 reshape2_1.4.4 tidyselect_1.2.0 rlang_1.1.2
[61] munsell_0.5.0 cellranger_1.1.0 tools_4.2.0 xgboost_1.7.5.1
[65] cli_3.3.0 generics_0.1.3 stringr_1.4.0 yaml_2.3.5
[69] sparseMatrixStats_1.8.0 R.oo_1.25.0 compiler_4.2.0 rstudioapi_0.13
[73] beeswarm_0.4.0 curl_4.3.2 png_0.1-7 tibble_3.2.1
[77] statmod_1.5.0 stringi_1.7.6 lattice_0.20-45 bluster_1.6.0
[81] assertive.base_0.0-9 vctrs_0.6.4 pillar_1.9.0 lifecycle_1.0.4
[85] rhdf5filters_1.8.0 BiocManager_1.30.17 combinat_0.0-8 GlobalOptions_0.1.2
[89] RcppAnnoy_0.0.21 BiocNeighbors_1.14.0 data.table_1.14.2 bitops_1.0-7
[93] irlba_2.3.5.1 rtracklayer_1.56.1 assertive.types_0.0-3 R6_2.5.1
[97] BiocIO_1.6.0 assertive.properties_0.0-5 vipor_0.4.5 codetools_0.2-18
[101] MCMCprecision_0.4.0 MASS_7.3-57 rhdf5_2.40.0 rjson_0.2.21
[105] withr_2.5.0 GenomicAlignments_1.32.1 Rsamtools_2.12.0 GenomeInfoDbData_1.2.8
[109] parallel_4.2.0 hms_1.1.1 beachmat_2.12.0 DelayedMatrixStats_1.18.2 [113] Rtsne_0.16 pROC_1.18.5 ggbeeswarm_0.7.2 restfulr_0.0.15

decontX celda • 406 views
Entering edit mode

We have just upgraded the celda package to remove the dependencies that are no longer available on CRAN. Please make sure you are using version 1.18.1 which was just released in Bioc 3.18 (R-4.3.1) a few days ago.

Entering edit mode
Last seen 1 day ago
United States

You should upgrade to R-4.3.1 and Bioc 3.18 and try again. Let us know if you still have the same problem after upgrading.

Entering edit mode

Thank you for your quick and helpful response. Reached out to the higher-ups to see if I can install the new version of R onto our group's server. If you don't hear from me again, no news will be good news!

Entering edit mode
Last seen 10 days ago
United Kingdom

There is an incompatibility of irlba and the most recent version of Matrix. A temporary solution is to downgrade Matrix, see here.


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