In a given experiment I am modeling
~0 + treatment*time + cell_type, for which I have
T2, ...) and
cell2, ...). Given that I'm looking at the interaction of
time, not all individual factors will be available (e.g.
t1) since these are given as linear combinations of the interactions (
When I do:
fit <- lmFit(df, design)
I can then extract the coefficients with
treatmentTreated timeT2 timeT3 ... treatmentTreated.timeT2 gene1 -1.34 2.34 1.23 ... 3.45 gene2 -2.44 3.12 0.23 ... 9.12 gene3 -0.37 1.59 0.76 ... 0.43 ...
Now the issue is that I'd like to extract all coefficients but I do not have those for
timeT1, as those will be given by a linear combination of the other columns (or rather, the inverse). I'm wondering how I can extract those given that I have no intercept? What am I missing in the interpretation of this? Thanks in advance