Question

DESeq2 using 'relevel' for different comparisons

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Matan G. ▴ 60

@matan-g-22483

Last seen 3.3 years ago

Let's say that I have RNA seq data with multiple clinical conditions from multiple patients/samples. As far as I understand, the first level that is used is the reference level that other conditions will be compared to. For example if I have the following conditions: 1. Control 2. Treatment 1 3. Treatment 2

One option is to put the "control" as the first level that the other conditions will be compared to separately: Treatment 1 vs control Treatment 2 vs control

The question: If I want to compare the treatments (i.e. Treatment 1 vs Treatment 2), what's the level that should be run first as the reference level?

Thanks

deseq2 • 1.7k views

ADD COMMENT • link updated 5.0 years ago by Michael Love 43k • written 5.0 years ago by Matan G. ▴ 60

score 0 · Answer 1 · 2019-12-03

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Michael Love 43k

@mikelove

Last seen 2 hours ago

United States

You can just use the contrast argument. See the vignette and ?results

ADD COMMENT • link 5.0 years ago Michael Love 43k

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Thank you for the prompt reply. I have read the contrast argument section.

If you use the contrast argument you discard the relevel (ie deactivate it)?
In one of the vignettes, it written that there is a great importance for writing the control/reference first. How does the contrast argument take it into consideration?
Is putting treatment 1 as the first level statistically make sense when comparing it to treatment 2?

Best

ADD REPLY • link 5.0 years ago Matan G. ▴ 60

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By default, R will choose a reference level for factors based on alphabetical order. Then, if you never tell the DESeq2 functions which level you want to compare against (e.g. which level represents the control group), the comparisons will be based on the alphabetical order of the levels. There are two solutions: you can either explicitly tell results which comparison to make using the contrast argument (this will be shown later), or you can explicitly set the factors levels.

ADD REPLY • link 5.0 years ago Michael Love 43k