scran normalize

[jayypaul]

Hello,

I have a heterogeneous dataset consisting of stroma and immune cells. For now, I'm interested in the stroma cells, and I was wondering if running scran again after subsetting the compartment of interest will lead to more accurate size factor estimation, since heterogenous data can produce negative estimates in some cases (which I witnessed but was able to address).

After subsetting, I have this many cells per sample:

And I would imagine that this would be a problem as well. Prior to subsetting I have this many cells per sample:

I've also read that low number of cells per sample could be problematic with scran normalization... but just want to get some opinion from authors on which may be the better route forward.. run norm prior to subset, then subset? Or re run...

Thanks!