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Question: Raw count data for SC3 and SingleCellExperiment set problem
1
10 months ago by
chengyuzou10
chengyuzou10 wrote:

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...

modified 10 months ago by Vladimir Kiselev130 • written 10 months ago by chengyuzou10
2
10 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:

For the SingleCellExperiment side: the error message is telling you that it can't find the relevant assay. This means that your SingleCellExperiment doesn't have a matrix named normcounts in the assays slot, hence normcounts(sce) fails. Admittedly the error message could be more informative, though any suggestions in this regard should be directed to the SummarizedExperiment maintainers.

Regarding the featureNames error; I don't know where that comes from. Make sure you're using the latest version of scater (1.6.something). And when asking questions, it is usually proper to post a minimum working example and your session information, see http://www.bioconductor.org/help/support/posting-guide/.

2
10 months ago by
Sanger Institute, Cambridge, UK