How should I define contrast with more than 2 levels in DESeq2 ?

Question

[star]

I would like to do differential expression analysis using DESeq2 while my contrast has more that 2 levels! I faced the problem which was how to define it in result function. How should I define this type of factors with many levels?

Thanks in advance.

[Devon Ryan]

There are multiple ways of specifying a contrast, possibly the most relevant of which to you is a vector of the form c(0, 0, 1, 1, -1, -1, 0, 0), which are the signs to use on multiple coefficients in a contrast. If that and the reply from abc don't clarify things, then post an exact example of an experiment and the contrast you need to specify.

Answer 1

[Ati]

You have to use "name" argument in "result" function which is the name of the individual effect (coefficient) for building a results table. Use this argument rather than contrast for continuous variables, individual effects or for individual interaction terms.