Error in testEmptyDrops(m, lower = lower, ...) : no counts available to estimate the ambient profile

[Xietingyan]

Hi Aaron,
I use the DropletUtils package to filter single cell data.
I have encountered this problem .

tmpdir = setwd("F:/sample208_filtered_feature_bc_matrix")
dir.name <- tmpdir
list.files(dir.name)
"barcodes.tsv" "genes.tsv" "matrix.mtx"

sce <- read10xCounts(dir.name,col.names = TRUE)
sce
class: SingleCellExperiment
dim: 32738 11701
metadata(0):
assays(1): counts
rownames(32738): ENSG00000243485 ENSG00000237613 ... ENSG00000215616
ENSG00000215611
rowData names(3): ID Symbol NA
colnames(11701): AAACCCAAGACAAGCC-1 AAACCCAAGCTGTACT-1 ... TTTGTTGTCGATACGT-1
TTTGTTGTCTCTGACC-1
colData names(2): Sample Barcode
reducedDimNames(0):
spikeNames(0):

set.seed(100)
e.out <- emptyDrops(counts(sce))
Error in testEmptyDrops(m, lower = lower, ...) : no counts available to estimate the ambient profile

I don't know this problem about relativing "rowData names(3):ID Symbol NA"

I will appreciate any advice on how to solve this.
Many thanks
Janexty

[LTLA]

Have a look at #14 and https://support.bioconductor.org/p/123554/#123562.

[Xietingyan]

Yes, thank you very much.

[LTLA]

I'm going to assume that this was resolved.

[hk20013106]

Hi I'm having the same issue and I'm using the BD Rhapsody scRNA data.

We sequenced 100G, and obtained maybe 9000 nuclei (not cell).

I'm not 100% sure, but I'm using the only matrix which I assume is the raw.
I change the lower to 150 or 200 which work well. But the results are different.
I understand that "lower" is the total umi per nuclei in my case, but not sure how can I decide this parameter since it highly affects the result?

Thanks!

[LTLA]

Please open a new issue.