# scater: SingleCellExperiment, Error in seq_len(ncol(assay))

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 seq_len(ncol(assay)) : first element used of 'length.out' argument


Any help would be greatly appreciated.

• 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.
– benn
Dec 11, 2017 at 8:41
• 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
– llrs
Dec 11, 2017 at 9:05

library(SingleCellExperiment)