makeContrastsDream for Interaction
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abadgerw • 0
@5088ef59
Last seen 2 hours ago
United Kingdom

I am interested in the interaction between a stimulation of various cell lines and a specific genotype. I am particularly interested in the following contrasts:

  1. Differences between genotypes without stimulation (both Con HLA Pos vs Con HLA Neg and PDL HLA Pos vs PDL HLA Neg conditions)
  2. Differences between genotypes with stimulation (Fib HLA Pos vs Fib HLA Neg)

Therefore, I planned to run an interaction model like this:

form <- ~ 0 + HLA*Stim + (1 | ID)

However, I am stuck on how to setup contrasts for this more complex model. I'm sharing my metadata here for reference: enter image description here

Any insight into the call I can make to makeContrastsDream for this interaction analysis? I looked at the examples provided online for making contrasts but didn't see an example with an interaction to follow.

limma DifferentialExpression variancePartition dream • 103 views
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gabriel.hoffman any insight?

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