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I am having a SingleCellExperiment (sce) object:

sce <- SingleCellExperiment(list(counts=UMI_count))

which has two dimensions:

dim(sce)
[1] 46761 68027

When I am trying to get column sums for all rows the following does not work:

colSums(assay(sce), na.rm = FALSE, dims = 1)

Giving me an error:

Error in colSums(assay(sce)) : 'x' must be an array of at least two dimensions

Apparently the issue was already described:

https://support.bioconductor.org/p/100954/

However, I can not find the solution. Is there another way of getting sums of columns of either SingleCellExperiment object or just dgcMatrix?

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  • $\begingroup$ Are you trying to get the sum of the rows or the columns? $\endgroup$ – AudileF Dec 20 '17 at 9:09
  • $\begingroup$ Did you check what does assay(sce) return? Which is the output of dim(assay(sce)) ? $\endgroup$ – llrs Dec 21 '17 at 8:17
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Ultimately I just implemented it manually with the precursor to SingleCellExperiment matrix (UMI_count which is dgcMatrix type) object in the following way:

# Removing genes with 0 - counts in all of the columns
num_removed = 0
for(i in 1:nrow(UMI_count)) {
  idx = i - num_removed
  if(sum(UMI_count[idx,]) < 1) {
    UMI_count <- UMI_count[-idx,]
    num_removed = num_removed + 1
    print(i)
  }
}

sce <- SingleCellExperiment(list(counts=UMI_count))

I am getting sums of the columns for each row and then filtering out rows with the sum < 1. So, sum function for the slices - rows (numeric type) is working.

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