How does DESeq2 handle multiple conditions in one design.
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grsyhhsb • 0
@cdb4b488
Last seen 14 months ago
United States

As an example, if the study design is treatment, and there are 3 different groups of samples in the study, treatment A, treatment B, and treatment C. I know I can get pair-wise comparison by using results(dds, contrast=c("condition","Treatment A","Treatment B"), but I'm curious about how DESeq2 does that. Is DESeq2 constructing a linear model for each gene and each of the 3 conditions and comparing their coefficient pair-wise? Thanks.

DESeq2 • 420 views
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@mikelove
Last seen 1 hour ago
United States

Yes but is it also sharing the dispersion (variance) parameter, there is a FAQ on this in the vignette.

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