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...?)

I ran it as you suggested. The results have similarities to what I get from DESeq2.

Is there something I need to take into account if I used the WithSpikes = FALSE option (as my data lacks spike-ins)?