CellAnnotation in scRNA-seq experiment with R (4.0.5) using Seurat (4.0) library

[Emiliano-Juarez]

Hello Bharat's lab, I think it is an amazing job what you did!

I've got a little problem at the moment when I want to annotate or identify the clusters, due to you grouped four different sets (immune, epithelial, stromal and global). I shall wish to know how I can do it or how you did it.
PD: I am using RStudio (4.0.5) and Seurat (4.0) library in order to analyze the dataset.

Thanks and regards EJL.

[mxposed]

Thank you for your interest!

What problem do you have specifically? The processed datasets are published on GEO along with just metadata annotation, if you want to just reuse the data. To load data in Seurat, please see this package

If you want to rerun the analysis, you need to follow the code in this repository, and it's not in R/Seurat.

[Emiliano-Juarez]

Ok, i.e. When I try to annotate the clusters with the [email protected]$Cell.Type it gave me the following error.

the attribute 'names' [18] must to have the same length as the vector [15]

[mxposed]

This error generally means that the dimensions of left-hand side and right-hand side of assignment are not the same.

If you post your code, I might be able to tell why this problem comes up

[Emiliano-Juarez]

Of course.
`stromal = readRDS ("seurat_objects/complete_data_stromal.rds")
stromal.ids = levels ([email protected]$Cell.Type)

names(stromal.ids) = levels (stromal)
Error in names(stromal.ids) = levels(stromal) :
the attribute 'names' [18] must to have the same length as the vector [15]`

[mxposed]

Sorry, I cannot determine from the code what you were trying to do.