How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
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kyusikkim • 0
@kyusikkim-14167
Last seen 3 months ago
United States

Hello all!

The experiment I am analyzing has 2 strains (WT/TS), 2 conditions (A/B), and 2 "assays" (riboseq/rnaseq). I am looking to get the effect of the condition normalized for strain and RNA-seq differences. Would I be correct in assuming a 2x2x2 experiment structure and so the design I want is ~ strain + condition + assay + strain:condition:assay? Do I need to add the three dual interactions of strain:condition + strain: assay + condition:assay?

Thanks for your guys' time and help!

DESeq2 RiboSeq RNASeq • 107 views
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@mikelove
Last seen 21 hours ago
United States

That would be one way to set up the design, but there are actually a lot of considerations into how to set up the analysis here, and I have to limit myself to software related questions due to time constraints.

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