Question: limma interaction term
0
gravatar for PJ
3.3 years ago by
PJ0
United States
PJ0 wrote:

Hi everybody,

I have a model with 2 main factors and its interaction:

designmodel = model.matrix(~0 + Factor1 + Factor2 + Factor1:Factor2)

Factor 1 has two levels and factor 2 has 4 levels. My question is if when I test the interaction term I can add all 8 groups as follow: 

contrastInteraction = makeContrasts(((Factor1.Level1Factor2 - Factor1.Level2Factor2 - Factor1.Level3Factor2 - Factor1.Level4Factor2 ) - (Factor2.Level1Factor2 - Factor2.Level2Factor2 - Factor2.Level3Factor2 - Factor2.Level4Factor2)),  levels=design)

Or shoud I test the interaction in 4 separate contrasts (one for each level of factor 2)? Thanks for you advice!

PJ 

limma interaction model • 717 views
ADD COMMENTlink modified 3.3 years ago by Gordon Smyth38k • written 3.3 years ago by PJ0
1

You don't provide a lot of details - what's your experimental design? What does Factor1 or Factor2 contain? - so it's hard to tell what the coefficient names mean, let alone whether you're doing something sensible with your contrasts.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Aaron Lun25k
Answer: limma interaction term
0
gravatar for Gordon Smyth
3.3 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

You model has 3 degrees of freedom for interaction. To test for interaction you would do:

fit <- lmFit(y, design)
fit <- eBayes(fit)
topTable(fit, coef=6:8)

There is no need to use makeContrasts().

Note that you must test all 3 df together. Trying to do separate tests for individual interaction contrasts has no meaning.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Gordon Smyth38k
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