CreateSeuratObject function for scRNA seq data doesn't give the nCount_RNA & nFeature_RNA in the returned object ??

[STafrimR]

Does any one knows were the problem is?

I use publicly available scRNA seq data (folder with 3 required files : barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

Code:

df <- Read10X (data.dir = "../path_to _folder/")

obj <- CreateSeuratObject ( counts= df, project= "df", min.cells =3, min.features=200)

then returns just a SeuratObject not containing nCounts_RNA and nFeature_RNA, Just the barcodes in row and a column with orig.ident,

the meta data:

Thank you

[AlexisW]

Do you have a value for getOption("Seurat.object.assay.calcn") ?

Can you try recreating the object in a fresh session? What if you explicitly set: options(Seurat.object.assay.calcn = TRUE) before running CreateSeuratObject()?

To make sure you're in an isolated environment, you can try running a minimal example in reprex:

library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> 
#> Attaching package: 'SeuratObject'
#> The following object is masked from 'package:base':
#> 
#>     intersect

cnts <- matrix(c(0,0,1,0,2,0,0,0,0),
               nrow = 3,
               dimnames=list(letters[1:3], LETTERS[1:3])) |>
  as("dgCMatrix")

obj <- CreateSeuratObject(counts = cnts)

head(obj)
#>      orig.ident nCount_RNA nFeature_RNA
#> A SeuratProject          1            1
#> B SeuratProject          2            1
#> C SeuratProject          0            0

^{Created on 2024-02-15 with reprex v2.0.2}

Also, what is your version of Seurat and SeuratObject? Run sessionInfo() after a library(Seurat) call.

[STafrimR]

Hi AlexisW

Thank you again.

It seems that I had a problem with the tidyverse, its was not the newest version, and after updating the CreateSeuratObject() function worked perfectly.

[AlexisW]

I don't see why the tidyverse has any role to play here, but great that it worked!