Exactly, those. It seems really restrictive to throw away or treat as arbitrary dispersion differences between cells (regrettably common) and between genes (less common, and oversimplified on its face, I think)
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Sure. My reservation is just that baking pretty severe and unusual misspecification into the model might make those unreliable or unstable. The same goes for ZI models (which, as far as I know, still have no mechanism or direct evidence).
I fail to see how this is unusual, it's a standard model. As for reliability and stability, I believe that we make a good case for them in the paper for our model. I have my own thoughts on ZI models but I'll save them for another time as here we do not model ZI.
Of course it could be useful in other applications (e.g., DE) to have genewise dispersions and it's something that we could add in a future version of the package.
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