I have an experiment with 3 factors: cell_type (
cell10), time (
t7) and treatment (
treated). I'm modeling it as
~0 + time*treatment + cell_type, and my resulting design matrix has columns:
cell2. Note how I do not have independent columns for
treated only, This is to make it easier to handle the contrasts, in which case I am combining multiple columns if I just want to compare
treated. But I digress.
My question is the following: I want to analyze the coefficients at different times or treatments. For this I can extract my
fit$coefficients object resulting from
lmFit, but then I get coefficients with the same columns as my design matrix, i.e. coefficients for columns
control.t2, ..... But I want to extract a representative coefficient of
t2, etc irrespective of
treatment. For instance, I want to take the coefficients at time 1 so both
treated.t1, but I'm not sure how I can combine the coefficients. I.e. I want to analyze the
t1 coefficient irrespective of treatment.
I'm guessing that it should be possible to alter the design matrix to represent the individual effects but it would fail since the column for
t1 would basically be given by
control.t1 + treatment.t1 (and the same for all time points), in which case the model would not be fittable. I'm also thinking that alternatively I could compute the mean of the coefficients
treatment.t1, but not sure how accurate this would be. Any suggestions?