I have two groups of cells with two predefined phenotypes. There are 30 in each group (60 in total) and I wanted to use BASiCS to perform differential expression between the two groups. How do I go about it?

The vignette suggests providing two chains into the DE-function of BASiCS. Does that mean that I have to run MCMC for each subgroup separately and then do DE providing each group separately?

Or do I run MCMC on the whole group of cells (60) and then split them into two chains, one for each group? I haven't found a was to subset a chain yet (maybe it is not possible...?)

Yes, you should run `BASiCS_MCMC` separately for each group of samples and then use those as the input of `BASiCS_TestDE`. Let me know if you have any issues while running the analysis.

Indeed, I will expect that DESeq2 and BASiCS report similar results when assessing changes in mean expression between the groups. Said this, the main advantage of using BASiCS is the differential variability testing (through over-dispersion or, more recently, residual over-dispersion https://www.biorxiv.org/content/early/2017/12/21/237214). Moreover, downstream analysis should not be affected by the lack of spikes (as seen in the biorXiv pre-print, the spikes and non-spikes models lead to very similar posterior inference).