Cannot add new cells with NormalizeData from seurat

Question

[Adrian]

Hi,

I'm tried running NormalizeData with a seurat object created from raw matrix files of cellranger outs, however it returns an error:

WT1 <- NormalizeData(object = WT1)
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in `[[<-`:
! Cannot add new cells with [[<-

I also tried to filter the seurat object and it returned no cell found

WT_filtrial <- subset(x = WT,  subset= (nUMI >= 500) &  (nGene >= 250) &    (log10GenesPerUMI > 0.80) & (mitoRatio < 0.05)) 
Error in `subset()`: ! No cells found

I'm able to just filter the metadata in the seurat, but not the object directly

Ho_fil <- subset(x = [e-mail], subset= (nUMI >= 500))

I believe these all indicate similar problem?

Thanks in advance

[bk11]

Can you show your Seurat object (WT1)? Is the active assay "RNA" in your Seurat object? If not you may have to change the default assay to something else DefaultAssay(WT1) <- "something". [Note: "something" could be for e.g., integrated, spatial etc.].