Question: The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
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gravatar for 2002ymx02
4 weeks ago by
2002ymx020
Germany, Dresden, TUD
2002ymx020 wrote:

Hi Prof. Gordon Smyth,

I have a question about the meaning of interaction terms in design matrix on the page 38 in the edgeR User's Guide. In line 19, the guide say: "The last two coefficients give the DrugvsPlacebo.1h and DrugvsPlacebo.2h contrasts". But my understanding is that the last two coefficients ( [5] "TreatDrug:Time1h", [6] "TreatDrug:Time2h" in model.matrix(~Treat * Time, data=targets)) could be the difference of difference, which means the effects (Drug.1h-placbo.1h)-(Drug.0h-placebo.0h) and (Drug.2h-placbo.2h)-(Drug.0h-placebo.0h). (Drug.0h-placebo.0h) is the reference level for interaction. Is my understanding right?

Best, Mingxing Yang

edger • 61 views
ADD COMMENTlink modified 4 weeks ago by Gordon Smyth38k • written 4 weeks ago by 2002ymx020
Answer: The meaning of interaction terms in design matrix in edgeR User's Guide on page
0
gravatar for Gordon Smyth
4 weeks ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

I appreciate your reading the edgeR User's Guide so carefully.

Yes, your understanding is correct but so is the edgeR User's Guide.

The DrugvsPlacebo.1h and DrugvsPlacebo.2h contrasts are defined on page 36 of the Guide, and they are exactly equivalent to what you say they should be.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Gordon Smyth38k

Thank you for your time, Gordon. Actually, my understanding of interaction terms [5] "TreatDrug:Time1h", [6] "TreatDrug:Time2h" are (Drug.1h-placbo.1h)-(Drug.0h-placebo.0h) and (Drug.2h-placbo.2h)-(Drug.0h-placebo.0h) respectively, which are different from the definition on page 36 of the Guide: DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h), DrugvsPlacebo.2h = (Drug.2h-Drug.0h)-(Placebo.2h-Placebo.0h)

That is why I asked this question. Because this is very confusing and only a few people understand this, that is why I only asked you this question.

Best, Mingxing Yang

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by 2002ymx020

Simple arithmetic shows you that the two expressions are exactly the same:

(Drug.1h - Placbo.1h) - (Drug.0h - Placebo.0h)

= Drug.1h - Placebo.1h - Drug.0h + Placebo.0h

= (Drug.1h - Drug.0h) - (Placebo.1h - Placebo.0h)

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Gordon Smyth38k

Many thank, Gordon. Yes, they are the same.

ADD REPLYlink written 4 weeks ago by 2002ymx020
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