May I ask if SC3 is suitable for raw count matrix generated by Dropseq/Indrop? Usually the output of them are not FPKM count matrix as suggested in the package manual.
Also, I got an issue with SingleCellExperiment issue. When I use the function normcounts(sce), an error shows up like
Error in assay(object, i = exprs_values) :
'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i'
'i' not in names(assays(<SingleCellExperiment>))
or if I calculate CPM here as calculateCPM(sce, use.size.factors = FALSE)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘featureNames’ for signature ‘"SingleCellExperiment"’
Both of the mistakes are shown up even if use the example data embedded in the scater package as guided by the tutorial (https://www.bioconductor.org/packages/devel/bioc/vignettes/scater/inst/doc/vignette-intro.html)
Based on the mistakes on scater/singlecellexperiment set, I just could not start with SC3...