Biostars beta testing.
Question: How should I define contrast with more than 2 levels in DESeq2 ?
2
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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.

ADD COMMENTlink 3.2 years ago star • 150 • updated 3.2 years ago abc • 30
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1

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.

ADD REPLYlink 3.2 years ago
Devon Ryan
90k
0
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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.

ADD COMMENTlink 3.2 years ago abc • 30

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