Errors with SeuratObject, and Matrix

[MeganRMonaghan]

Hi! I seem to be caught in a catch 22. I am currently analysing some single cell RNA seq data and despite the code running smoothly I now have a cycle of two errors. After updating Seurat to version 5.01, I receive the following error when I attempt to produce my SeuratObject

cns.sce <- CreateSeuratObject(counts(rna_sce)[, which(colnames(rna_sce) %in% common.cells)])

Warning: Data is of class dgTMatrix. Coercing to dgCMatrix. Error in validObject(.Object) : invalid class "LogMap" object: Duplicate rownames not allowed

I have seen in other posts here this was an issue with Matrix, so I used the following code, and am met with this error continuously, to the extent where I cannot see what I am typing in the console as the error repeats hundreds of times over.

devtools::install_version("Matrix",version = "1.6-1.1")
library(Matrix)

Loading required package: SeuratObject
Error: package or namespace load failed for 'SeuratObject' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace 'Matrix' 1.6-1.1 is already loaded, but >= 1.6.3 is required

To stop this error, I have to uninstall Matrix 1.6-1.1 and restart the session, which returns me to the original error once I update Matrix.

Warning: Data is of class dgTMatrix. Coercing to dgCMatrix. Error in validObject(.Object) : invalid class "LogMap" object: Duplicate rownames not allowed

Any help here would be greatly appreciated as I cannot work on my data at present due to this.

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

time zone: Australia/Adelaide
tzcode source: system (glibc)

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

other attached packages:
[1] Matrix_1.6-4 Seurat_5.0.1 ensembldb_2.24.1 AnnotationFilter_1.24.0 GenomicFeatures_1.52.2
[6] AnnotationDbi_1.62.2 Biobase_2.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.0 IRanges_2.36.0
[11] S4Vectors_0.40.1 SeuratObject_5.0.1 sp_2.1-2 AnnotationHub_3.8.0 BiocFileCache_2.8.0
[16] dbplyr_2.4.0 BiocGenerics_0.48.1

loaded via a namespace (and not attached):
[1] fs_1.6.3 ProtGenerics_1.32.0 matrixStats_1.1.0 spatstat.sparse_3.0-3
[5] bitops_1.0-7 devtools_2.4.5 httr_1.4.7 RColorBrewer_1.1-3
[9] profvis_0.3.8 tools_4.3.2 sctransform_0.4.1 utf8_1.2.4
[13] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16 urlchecker_1.0.1
[17] prettyunits_1.2.0 gridExtra_2.3 progressr_0.14.0 cli_3.6.1
[21] spatstat.explore_3.2-5 fastDummies_1.7.3 spatstat.data_3.0-3 ggridges_0.5.4
[25] pbapply_1.7-2 Rsamtools_2.16.0 parallelly_1.36.0 sessioninfo_1.2.2
[29] limma_3.58.1 rstudioapi_0.15.0 RSQLite_2.3.4 generics_0.1.3
[33] BiocIO_1.10.0 ica_1.0-3 spatstat.random_3.2-2 dplyr_1.1.4
[37] fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4 yaml_2.3.7
[41] edgeR_3.42.4 SummarizedExperiment_1.32.0 SparseArray_1.2.0 Rtsne_0.17
[45] grid_4.3.2 blob_1.2.4 promises_1.2.1 dqrng_0.3.2
[49] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.22-5 beachmat_2.18.0
[53] cowplot_1.1.1 KEGGREST_1.40.1 pillar_1.9.0 metapod_1.8.0
[57] rjson_0.2.21 future.apply_1.11.0 codetools_0.2-19 leiden_0.4.3.1
[61] glue_1.6.2 data.table_1.14.10 remotes_2.4.2.1 vctrs_0.6.5
[65] png_0.1-8 spam_2.10-0 gtable_0.3.4 cachem_1.0.8
[69] S4Arrays_1.2.0 mime_0.12 survival_3.5-7 SingleCellExperiment_1.24.0
[73] statmod_1.5.0 bluster_1.10.0 interactiveDisplayBase_1.38.0 ellipsis_0.3.2
[77] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-163 usethis_2.2.2
[81] bit64_4.0.5 progress_1.2.3 filelock_1.0.2 RcppAnnoy_0.0.21
[85] rprojroot_2.0.4 irlba_2.3.5.1 KernSmooth_2.23-22 colorspace_2.1-0
[89] DBI_1.1.3 tidyselect_1.2.0 bit_4.0.5 compiler_4.3.2
[93] curl_5.2.0 BiocNeighbors_1.20.0 xml2_1.3.6 DelayedArray_0.28.0
[97] plotly_4.10.3 rtracklayer_1.60.1 scales_1.3.0 lmtest_0.9-40
[101] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.33 goftest_1.2-3
[105] spatstat.utils_3.0-4 XVector_0.42.0 htmltools_0.5.7 pkgconfig_2.0.3
[109] sparseMatrixStats_1.14.0 MatrixGenerics_1.14.0 fastmap_1.1.1 rlang_1.1.2
[113] htmlwidgets_1.6.4 shiny_1.8.0 DelayedMatrixStats_1.24.0 zoo_1.8-12
[117] jsonlite_1.8.8 BiocParallel_1.36.0 BiocSingular_1.18.0 RCurl_1.98-1.13
[121] magrittr_2.0.3 scuttle_1.12.0 GenomeInfoDbData_1.2.11 dotCall64_1.1-1
[125] patchwork_1.1.3 munsell_0.5.0 Rcpp_1.0.11 reticulate_1.34.0
[129] stringi_1.8.2 zlibbioc_1.48.0 MASS_7.3-60 plyr_1.8.9
[133] pkgbuild_1.4.3 parallel_4.3.2 listenv_0.9.0 ggrepel_0.9.4
[137] deldir_2.0-2 Biostrings_2.68.1 splines_4.3.2 tensor_1.5
[141] hms_1.1.3 locfit_1.5-9.8 igraph_1.5.1 spatstat.geom_3.2-7
[145] RcppHNSW_0.5.0 reshape2_1.4.4 biomaRt_2.56.1 ScaledMatrix_1.10.0
[149] pkgload_1.3.3 BiocVersion_3.17.1 XML_3.99-0.15 scran_1.28.2
[153] BiocManager_1.30.22 httpuv_1.6.13 RANN_2.6.1 tidyr_1.3.0
[157] purrr_1.0.2 polyclip_1.10-6 future_1.33.0 scattermore_1.2
[161] ggplot2_3.4.4 rsvd_1.0.5 xtable_1.8-4 restfulr_0.0.15
[165] RSpectra_0.16-1 later_1.3.2 viridisLite_0.4.2 tibble_3.2.1
[169] memoise_2.0.1 GenomicAlignments_1.36.0 cluster_2.1.4 globals_0.16.2
[173] here_1.0.1

[mhkowalski]

Hello,

This may not be related to the Matrix package. I see from your output that you are getting the error message Duplicate rownames not allowed. Can you check if there are duplicate row names in the counts matrix you are providing to CreateSeuratObject?

For instance, what is sum(duplicated(rownames(count_matrix)))?

[MeganRMonaghan]

Hello,

This may not be related to the Matrix package. I see from your output that you are getting the error message Duplicate rownames not allowed. Can you check if there are duplicate row names in the counts matrix you are providing to CreateSeuratObject?

For instance, what is sum(duplicated(rownames(count_matrix)))?

I'm seeing the following:

sum(duplicated(rownames(rna_sce)))
[1] 20

Which is unusual, as I did not have this issue with the duplicates the last time I ran this analysis.

[mhkowalski]

Ok, thanks for your response. This is likely causing the problem, as the row names of the matrix must be unique. Please either remove the duplicate rows or change the row names to ensure there aren't duplicates.

[erzakiev]

Error still pops up with all rownames being unique though. It's somewhat dataset-specific (only occurs sometimes) so here is a csv dataset where it does pop up

Guo <- read.csv(file = 'example.csv')
Guo <- CreateSeuratObject(counts = Guo, min.cells = 0, min.features = 0)

Error in validObject(.Object) : 
  invalid class “LogMap” object: Duplicate rownames not allowed

Relevant packages' versions:

[1] Matrix_1.6-4          Seurat_5.0.1          rhdf5_2.46.0          SeuratDisk_0.0.0.9021
[5] shiny_1.8.0           SeuratObject_5.0.1    sp_2.1-1

[Nicomakii]

Hi @erzakiev I am having the same exact issue with you, please let me know if you have resolved the problem. Thank you!

[pikapika505]

this is the problem I have had since I updated Seurat to V5. I running it on macOS Ventura 13.3. I still don't know how to resolve it. It's not caused by duplicates @mhkowalski

[chloe-shard]

I am also having the same issue - It's not caused by duplicates. I encountered this issue trying to run MetaFLUX analysis.

mean_exp=calculate_avg_exp(myseurat = sc_test_example,myident = 'Cell_type',n_bootstrap=3,seed=1)
Error in validObject(.Object) :
invalid class “LogMap” object: Duplicate rownames not allowed

[AHerik]

Also having this issue, not caused by duplicates and downgrading my version of Matrix has not helped. Would appreciate any fixes or advice.

Thanks!

[samIndeed]

Hi, I had the same issue and fixed it by making my column names unique!

I guess the problem (in my case anyway) is that the error says rownames instead of column names.

[nsauerwald]

Hi, I'm having the same issue with no duplicated row or column names. This never happened in previous versions of Seurat for me - this is with Seurat 5.0.1

sc701 <- CreateSeuratObject(counts = sc.data, project = "sample701", min.cells = 3, min,features = 200)
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Error in validObject(.Object) :
invalid class “LogMap” object: Duplicate rownames not allowed
sum(duplicated(colnames(sc.data)))
[1] 0
sum(duplicated(rownames(sc.data)))
[1] 0

[MomenehForoutan]

Hi team, I am having the same issue with Seurat v5.0.3 when trying to create Seurat object using CreateSeuratObject() function. The error says I have duplicated row names while I do not.
Thanks for any help with this in advance!
EDIT: it turned out that I also had duplicated column names but got the error for duplicated row names.

[apaikari]

Use options(Seurat.object.assay.version = 'v3') and it will work

[Ana1335]

I am having the same issue, any idea how to fix?

[shisang7]

just use seurat v4, and it will work