[R] Parameterisation of interaction terms in lm

[Luke Whitaker]

Hello,

I have a 2 factor linear model, in which the only terms I am interested 
in estimating and
testing are the interaction terms. I want to control for the main 
effects but have no interest
in estimating or testing them. However, I would like an estimate of the 
interaction effects
for every level of the interactions, whereas what I get is one fewer 
estimate than this, with the
first level apparently used as a baseline.

For example, suppose factor A has 2 levels, and factor B has 4 levels, I 
would like 4 estimates,
one for each level of B, showing how much different the actual A*B 
effect is from what it would
be if there were no interaction. I suspect it is necessary to assume the 
mean interaction is zero in
order to be estimable.

Although the experiment was designed to be balanced, there are some 
missing data, but no empty
cells. The experiment is actually a gene expression micro array, where A 
is tissue type and B represents
a number of genes of interest.

I have searched the archives, and read the docs relating to contrasts, 
but only succeeded in getting
confused. I would be very grateful if someone could point me to the 
solution.

Sincerely,

Luke Whitaker

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