Closed ssscj closed 5 years ago
computeSpikeFactors
, not computeSumFactors
.normalize()
step, everything gets re-normalized in plotCorrections.R
anyway.Thanks for your reply. I'm sorry for my mistake. I have one more question.
Can I skip the computeSpikeFactors()
step instead of normalize()
step, because I think the spike-ins are not important in the analysis.
The spike-ins are used for modelling variability in each batch. Now, that's not critical, but we already have the spike-ins in this data set, so why not use them? If you're referring to your own data set that doesn't have spike-ins, you can consider alternative strategies as described here.
thanks for developing this package While running
sce.emtab6<- computeSumFactors(sce.emtab,clusters=clusters1,min.mean=1)
it showedand while running:
sce.emtab3 <- normalize(sce.emtab2,return_log=FALSE)
it showedhow could I fix it? Thank you!