Closed kaizen89 closed 2 years ago
Thanks for posting! Welcome to cellpypes.
The error message looks like your counts are not integers (1,2,3,…) but decimals (1.2,1.9,…). I recommend using uncorrected raw UMI counts instead, i.e. read in the Cellranger output again and use that. I think uncorrected counts should work well: Ambient RNA contamination can be expected to affect all cell types the same and cellpypes‘ neighbour pooling should help to dampen its effects.
That is what I recommend as statistician. If you just want to test cellpypes on this very data, you can convert SoupX output to integer counts and the error message should go away. Option 1 for this: The SoupX authors recommend using ,roundToInt=TRUE‘ when you run SoupX correction with the ,adjustCounts‘ function. Option 2 for this quick&dirty approach: simply use ,round(SeuratObject::GetAssayData(lympho_NKT, "counts"))‘ in slot raw. Again, this option 2 is really to test cellpypes, not an analysis I would go for as rigorous scientist.
Did this make the error go away?
Starting with Seurat objects where the raw matrices are processed with SoupX, giving counts with decimals.
I get this error: