I get an error with perCellQC() that is related to the size of the data set, i.e. 10K cells work fine, 100K do not.
Can you elaborate a bit on what causes that?
> sce.all
class: SingleCellExperiment
dim: 32285 188814
metadata(1): Samples
assays(1): counts
rownames(32285): ENSMUSG00000051951 ENSMUSG00000089699 ...
ENSMUSG00000095019 ENSMUSG00000095041
rowData names(3): ID Symbol Type
colnames: NULL
colData names(2): Sample Barcode
reducedDimNames(0):
altExpNames(0):
> str(counts(sce.all))
Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
..@ i : int [1:309912166] 13 220 247 356 488 581 618 620 644 854 ...
..@ p : int [1:188815] 0 402 1246 1623 5412 9257 12937 17733 18766 19370 ...
..@ Dim : int [1:2] 32285 188814
..@ Dimnames:List of 2
.. ..$ : chr [1:32285] "ENSMUSG00000051951" "ENSMUSG00000089699" "ENSMUSG00000102331" "ENSMUSG00000102343" ...
.. ..$ : NULL
..@ x : num [1:309912166] 1 1 1 1 1 1 2 1 1 1 ...
..@ factors : list()
df.qc <- perCellQCMetrics(sce.all)
Error in validObject(.Object) : invalid class “RegularArrayGrid” object:
grid is too coarse (all grid elements must have a length <=
.Machine$integer.max)
I get an error with
perCellQC()
that is related to the size of the data set, i.e. 10K cells work fine, 100K do not. Can you elaborate a bit on what causes that?