cell_type not found when subsetting object

Question

cell_type not found when subsetting object

MjelleLab opened this issue 3 years ago · 3 comments

When running my whole Seurat object, run_de works fine. When I subset the object to contain only one cell type I get cell_type not found. What is the reason for this? I want to subset before running run_de to set different threshold for my cells types (High vs Low)

Answer 1 · 2022-04-13T19:18:42.000Z

Strange - can you send me a sample of the data? (email on profile).

Answer 2 · 2022-04-19T17:02:31.000Z

Error was related to number of cells. Setting a filter of min 100 cells solved it.

Answer 3 · 2024-08-19T11:04:10.000Z

libra_result = run_de(expr,meta = meta,

```
         replicate_col = "orig.ident",
```

         cell_type_col = "seurat_clusters",

         label_col = "RNA_snn_res.0.25",

```
         input_type = "scRNA",
```
```
         de_family = 'pseudobulk', 
```
```
         de_method = 'edgeR', 
```
```
         de_type = 'LRT',
```
```
         min_cells = 50,
```
```
         min_reps = 2,
```
```
         n_threads = 4
```
```
         )
```

Must group by variables found in .data.
✖ Column cell_type is not found. HOW TO FIX IT?