LTLA / scuttle

Clone of the Bioconductor repository for the scuttle package.
https://bioconductor.org/packages/devel/bioc/html/scuttle.html
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Error with perCellQC related to data set size: "grid elements must have a length <= .Machine$integer.max" #10

Closed friedue closed 3 years ago

friedue commented 3 years ago

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)
friedue commented 3 years ago

Nevermind; found Merv's post on this: https://github.com/Alanocallaghan/scater/issues/144

beachmat update solved it, indeed. Thanks!