Error in dimnamesGets(x, value) when trying to read data using Seurat package

I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function Read10X, I am getting this error

Error in dimnamesGets(x, value) : length of Dimnames[[1]] (45948) is not equal to Dim[1] (45947).

I am unsure how to resolve this issue.

R sessionInfo:

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] sp_1.5-0           SeuratObject_4.1.1 Seurat_4.1.1       Matrix_1.5-1

loaded via a namespace (and not attached):
  [1] nlme_3.1-153          spatstat.sparse_2.1-1 matrixStats_0.62.0    RcppAnnoy_0.0.19
  [5] RColorBrewer_1.1-3    httr_1.4.4            sctransform_0.3.4     tools_4.1.2
  [9] utf8_1.2.2            R6_2.5.1              irlba_2.3.5           rpart_4.1-15
 [13] KernSmooth_2.23-20    uwot_0.1.14           mgcv_1.8-38           rgeos_0.5-9
 [17] DBI_1.1.3             lazyeval_0.2.2        colorspace_2.0-3      tidyselect_1.1.2
 [21] gridExtra_2.3         compiler_4.1.2        progressr_0.11.0      cli_3.4.0
 [25] plotly_4.10.0         scales_1.2.1          lmtest_0.9-40         spatstat.data_2.2-0
 [29] ggridges_0.5.3        pbapply_1.5-0         goftest_1.2-3         stringr_1.4.1
 [33] digest_0.6.29         spatstat.utils_2.3-1  pkgconfig_2.0.3       htmltools_0.5.3
 [37] parallelly_1.32.1     fastmap_1.1.0         htmlwidgets_1.5.4     rlang_1.0.5
 [41] rstudioapi_0.14       shiny_1.7.2           generics_0.1.3        zoo_1.8-10
 [45] jsonlite_1.8.0        spatstat.random_2.2-0 ica_1.0-3             dplyr_1.0.10
 [49] magrittr_2.0.3        patchwork_1.1.2       Rcpp_1.0.9            munsell_0.5.0
 [53] fansi_1.0.3           abind_1.4-5           reticulate_1.26       lifecycle_1.0.2
 [57] stringi_1.7.6         MASS_7.3-54           Rtsne_0.16            plyr_1.8.7
 [61] grid_4.1.2            parallel_4.1.2        listenv_0.8.0         promises_1.2.0.1
 [65] ggrepel_0.9.1         deldir_1.0-6          miniUI_0.1.1.1        lattice_0.20-45
 [69] cowplot_1.1.1         splines_4.1.2         tensor_1.5            pillar_1.8.1
 [73] igraph_1.3.4          spatstat.geom_2.4-0   future.apply_1.9.1    reshape2_1.4.4
 [77] codetools_0.2-18      leiden_0.4.3          glue_1.6.2            data.table_1.14.2
 [81] png_0.1-7             vctrs_0.4.1           httpuv_1.6.6          polyclip_1.10-0
 [85] gtable_0.3.1          RANN_2.6.1            purrr_0.3.4           spatstat.core_2.4-4
 [89] tidyr_1.2.1           scattermore_0.8       future_1.28.0         assertthat_0.2.1
 [93] ggplot2_3.3.6         mime_0.12             xtable_1.8-4          later_1.3.0
 [97] survival_3.2-13       viridisLite_0.4.1     tibble_3.1.8          cluster_2.1.2
[101] globals_0.16.1        fitdistrplus_1.1-8    ellipsis_0.3.2        ROCR_1.0-11

single-cell seurat scrna-seq

• 3,027 views • link

updated 3.8 years ago by ATpoint

• written 3.8 years ago by cogen859 •

Cross-posted to bioinfo SE: https://bioinformatics.stackexchange.com/questions/19867/error-in-dimnamesgetsx-value-when-trying-to-read-data-using-seurat-package

Don't do this; it's bad etiquette and annoys people in both communities.

• 0 views • link

written 3.8 years ago by Ram

I am new to the forum, thank you for highlighting will keep in mind.

• 0 views • link

written 3.8 years ago by cogen859 •

1 answer

(45948) is not equal to Dim[1] (45947)

This is probably a mismatch between the count matrix and the annotation files. Check the head of the annotation files, there is probably a header line which is not expected by Read10X() as CellRanger returns headerless files.

• 0 views • link

written 3.8 years ago by ATpoint