Question: Add interaction term between variables to DEXSeq design
gravatar for zhenzuo2
11 months ago by
zhenzuo20 wrote:

I am trying to use DEXSeq::testForDEU() to compare two models with likelihood ratio test. The null model can be written as Y = β0 + β1 S + β2 T + ε and the full model can be written as Y = β0 + β1 S + β2 T + β_3 (S*T) + ε. In DEXSeq manual, it says "It must specify an interaction term between a variable from the sampleData columns with the ’exon’ variable". How can I add another interaction term between two variables to the full model? Current, I wrote the "fullModel" as "~sample + exon + S:exon + T:exon + S:T:exon" and "reducedModel" as "~sample + exon + S:exon + T:exon". Does it make sense to write full model's interaction term "S:T:exon" this way? Thank you.

dexseq interaction • 273 views
ADD COMMENTlink written 11 months ago by zhenzuo20

Hi zhenzuo2. Definitely, you can test the hypothesis that you wrote down using exactly the formulae that you mentioned.

ADD REPLYlink written 11 months ago by Alejandro Reyes1.7k
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