I've got an experiment with eight 10x scRNA-seq runs that I'm analysing by starting with something based on the simpleSingleCell workflow. I constructed each SingleCellExperiment with DropletUtils::read10xCounts()
.
I'm looking for any opinions or advice on when to combine these into one SingleCellExperiment object vs. having, say, a list of SingleCellExperiment objects (one per run)? I've been tossing up between a few options:
- Pass all runs via the
samples
argument ofDropletUtils::read10Counts()
and addingrun
to the colData - Filter each run (to remove empty drops) independently and then combine.
- Keep them separate until running something like
scran::mnnCorrect()
(which would seem to need a separate expression matrix for each run, anyway).
Thanks, Pete
Thanks, Aaron. Very helpful (as always).