I am trying to go through the following scRNA-seq tutorial.

But the line sce <- newSCESet(countData=all.counts) is not working anymore with the most up-to-date version of scater. Now we should use SingleCellExperiment function instead, so when trying to do the following:

sce <- SingleCellExperiment(assays = list(counts = all.counts))

I am getting the error:

Error in seq_len(ncol(assay)) : 
  argument must be coercible to non-negative integer
In addition: Warning message:
In seq_len(ncol(assay)) : first element used of 'length.out' argument

Any help would be greatly appreciated.

  • 1
    $\begingroup$ You can better ask questions about bioconductor packages on https://support.bioconductor.org/, you'll probably get an answer from Aaron Lun himself within a day. $\endgroup$
    – benn
    Dec 11, 2017 at 8:41
  • $\begingroup$ Which version of R and of the packages are you using? That workflow is for version 3.4 of Bioconductor, and the current version is 3.6 $\endgroup$
    – llrs
    Dec 11, 2017 at 9:05

2 Answers 2


I think you might want to use the most recent workflow, which should be for the latest version on Bioconductor.


You simply need to transform your data.frame into a matrix. Just use these two lines:

sce <- SingleCellExperiment(assays = list(counts = as.matrix(all.counts)))

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