Entering edit mode
3.5 years ago
LacquerHed
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30
Wondering if there is a good tutorial out the for differential expression analysis using interaction terms in Seurat with DESeq2? Like for instance if having two genotypes and two treatment conditions? Thanks!
Do you have biological replicates that allow pseudobulk-DE or do you strictly want to use the per-cell counts? I would probably simply take the matrix of raw UMI counts out of Seurat and then do the DESeq2 part manually once it goes beyond a simple two-group comparison. DESeq2 should be much faster after the next version (1.30.0, see https://github.com/mikelove/DESeq2/blob/master/NEWS) is being released due to addition of a new method to estimate the model parameters (from the glmGamPoi package).
I do have biological replicates that allow pseudobulk-DE. Thanks for the suggestion.
If for instance I did not have replicates, how would you go about using the per-cell counts for more complex comparisons? Have the DESeq2 interaction part down, just wondering about other options. Thanks.