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Posts by bvernot
Comment: C: Batch effects and model matrices
... Thanks for your thoughts, Mike. I was under the impression that ~genotype is a nested model of ~mouse, since it is just ~mouse constraining m1==m3 and m2==m4 (since those mice are the same genotype). But perhaps I'm wrong, or deseq2/monocle just can't handle that type of nesting? For what it's wo ...
... I have mice with two possible genotypes: homozygous wildtype for a gene of interest, or homozygous edited. We’ve collected cDNA of single cells from a few tissue types, although here I mostly ignore cell and tissue type. The primary issue is that I clearly have mouse-specific effects, but I don't k ...
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