**90**wrote:

Hello,

I hope someone can help me understand this better. I am running the emptyDrops method from DropletUtils library which distinguishes empty from non-empty cells. The function accepts lower parameter which specify the lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets. Link to manual.

Based on this, I thought that if I specified small number for lower, it will detect more non-empty cells and if used bigger number for lower, it will detect less non-empty cells. However, it didn't. In fact it is consistently detect more non-empty cells when lower is set to larger number. Am I missing something? Here is the code to reproduce the results.

```
library(DropletsUtils)
library(BiocFileCache)
bfc <- BiocFileCache("raw_data", ask = FALSE)
raw.path <- bfcrpath(bfc, file.path("http://cf.10xgenomics.com/samples",
"cell-exp/2.1.0/pbmc4k/pbmc4k_raw_gene_bc_matrices.tar.gz"))
untar(raw.path, exdir=file.path(tempdir(), "pbmc4k"))
library(DropletUtils)
fname <- file.path(tempdir(), "pbmc4k/raw_gene_bc_matrices/GRCh38")
sce <- read10xCounts(fname, col.names=TRUE)
set.seed(100)
e.out <- emptyDrops(counts(sce),lower=100)
sum(e.out$FDR <= 0.001, na.rm=TRUE)
[1] 4237
set.seed(100)
e.out.200 <- emptyDrops(counts(sce),lower=200)
sum(e.out.200$FDR <= 0.001, na.rm=TRUE)
[1] 4346
set.seed(100)
e.out.1000 <- emptyDrops(counts(sce),lower=1000)
sum(e.out.1000$FDR <= 0.001, na.rm=TRUE)
[1] 4326
set.seed(123)
e.out.test <- emptyDrops(counts(sce),lower=100)
sum(e.out.test$FDR <= 0.001, na.rm=TRUE)
[1] 4223
set.seed(123)
e.out.test <- emptyDrops(counts(sce),lower=200)
sum(e.out.test$FDR <= 0.001, na.rm=TRUE)
[1] 4316
set.seed(123)
e.out.test <- emptyDrops(counts(sce),lower=1000)
sum(e.out.test$FDR <= 0.001, na.rm=TRUE)
[1] 4324
```