Hi!

I have a SingleCellExperiment Object. I used the following code to normalise my data:

sce <- scran::computeSpikeFactors(sce, general.use = FALSE)
scater::normalise(sce)

I would like to retrieve the normalised matrix of count afterwards but could not find a proper way to do it. Can someone tell me where is it stored in this object ? 

Thank you in advance!

If you set return_log=FALSE in normalize, the "normalized counts" are available with normcounts(sce). Otherwise they're log-transformed and reported in logcounts(sce).