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Seurat not creating nCount_RNA and nFeature_RNA

Hey everyone,

I'm currently working on downstream analysis of single-cell RNA-Seq data, and I'm encountering an issue where the RStudio instance on my server is not properly creating the Seurat object with the nCount_RNA and nFeature_RNA columns, and only creating the object with orig.ident . This problem is not happening on my RStudio instance on my personal laptop, and when comparing the installed packages, they're identical. If anyone has encountered this issue and found a solution I'd greatly appreciate it. The following code is identical on both the server and laptop. The files are identical as well, with the files on my laptop being downloaded from the Linux server. Both instances have Seurat == 5.1.0.

library(Seurat)
library(celldex)
library(SingleR)
library(magrittr)
library(dplyr)

solote_matrix <- ReadMtx("matrix.mtx","barcodes.tsv","features.tsv", feature.column=1)
solote_seuratobj <- CreateSeuratObject(count=solote_matrix, min.cells=3, project="SoloTE")

Metadata on Linux:

enter image description here

Metadata on Laptop:

enter image description here

seurat rstudio
• 6,952 views • link
updated by bczvx1004 • bczvx1004 • written by Nicholas • Nicholas

Server:

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R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] dplyr_1.1.4                 magrittr_2.0.3              SingleR_2.2.0               celldex_1.10.1             
 [5] SummarizedExperiment_1.30.2 Biobase_2.60.0              GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [9] IRanges_2.34.1              S4Vectors_0.38.2            BiocGenerics_0.46.0         MatrixGenerics_1.12.3      
[13] matrixStats_1.3.0           Seurat_5.1.0                SeuratObject_5.0.2          sp_2.1-4

Personal Laptop:

R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] dplyr_1.1.4                 magrittr_2.0.3              SingleR_2.6.0               celldex_1.14.0              SummarizedExperiment_1.34.0
 [6] Biobase_2.64.0              GenomicRanges_1.56.1        GenomeInfoDb_1.40.1         IRanges_2.38.0              S4Vectors_0.42.0           
[11] BiocGenerics_0.50.0         MatrixGenerics_1.16.0       matrixStats_1.3.0           Seurat_5.1.0                SeuratObject_5.0.2         
[16] sp_2.1-4
• 0 views • link
written by Nicholas • Nicholas

1 answer

i had same problem today. i fix it with cleaning the workspace and restart the session by pressing the ctrl+shift+F10.

• 0 views • link
written by bczvx1004 • bczvx1004

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