Question: Differential expressiong with two groups in BASiCS
gravatar for muad.abdelhay
12 days ago by
muad.abdelhay10 wrote:

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...?)

ADD COMMENTlink modified 7 days ago by CataVallejos10 • written 12 days ago by muad.abdelhay10
gravatar for CataVallejos
11 days ago by
The Alan Turing Institute
CataVallejos10 wrote:

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.



ADD COMMENTlink written 11 days ago by CataVallejos10

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)?

ADD REPLYlink written 10 days ago by muad.abdelhay10
gravatar for CataVallejos
7 days ago by
The Alan Turing Institute
CataVallejos10 wrote:

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 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). 



ADD COMMENTlink written 7 days ago by CataVallejos10
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