The get.spikes argument in computeSumFactors only controls whether spike-in transcripts are filtered out in the deconvolution method, it doesn't switch over entirely to spike-in normalization.
Consider using r Biocpkg("scater") for package references, which links straight to the scater BioC page.
are -> is.
To normalize using ERCC spike-ins, you need to use
computeSpikeFactors
after settingisSpike
:The
get.spikes
argument incomputeSumFactors
only controls whether spike-in transcripts are filtered out in the deconvolution method, it doesn't switch over entirely to spike-in normalization.Consider using
r Biocpkg("scater")
for package references, which links straight to the scater BioC page.