How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions
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Hanan • 0
@c51d74dc
Last seen 23 days ago
Israel

Hello I have the following design in DESeq2: ~GT+TP+TP:GT . GT has two levels (K,W) . TP has two levels (0,2). I am looking for the genes that are up-regulated in samples where GT=W and TP=2. How do I define the contrast that these genes will have the highest log2FC. Thank you

DESeq2 • 172 views
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@mikelove
Last seen 1 day ago
United States

First, see the vignette section on interations, and the examples in ?results.

Beyond that, if you have further questions, setting up the statistical design is important. It's worth meeting with a local statistician or someone familiar with R to help you in this step. Unfortunately, I have to restrict my time on the support site to software related questions.