I have a single cell RNA-dataset and I used the deconvolution method for normalization. Now I want to extract the matrix with all normalized counts but it is not working. I tried the following:
sce <- computeSumFactors(sce, sizes=c(20, 40, 60, 400))
#Computing separate size factors for spike-in transcripts
sce <- computeSpikeFactors(sce, type="ERCC", general.use=FALSE)
#Applying the size factors to normalize gene expression
sce <- normalise(sce)
NormCounts = counts(sce, normalised = TRUE)
and the following error comes up:
> error in .local(object, ...) : unused argument (normalised = TRUE)
it is also not working with normalized = TRUE.
Where is my mistake? Does someone have a solution for this?
Thank you in advance!