Let's say that I am looking at the space of matrices $M_{n\times n}(\mathbb{R})$. If I have some linear function $F : M_{n\times n}(\mathbb{R}) \to M_{n\times n}(\mathbb{R})$, then I can take it's "trace" by taking a basis $\{ E_{ab} \}_{a,b=1}^{n} \subset M_{n\times n}(\mathbb{R})$ and evaluating the following: $$ \mathrm{Tr}(F) = \sum_{a,b=1}^{n} \left< E_{ab}, F(E_{ab}) \right>\ \ \ =?\ \ \ \sum_{a,b=1}^{n} \mathrm{Tr}\left[ F(E_{ab})^{T}E_{ab}\right] $$
I'm assuming that the inner product on $M_{n\times n}(\mathbb{R})$ I should be using is $ \left< A,B \right> = \mathrm{Tr}(B^{T}A)$.
But here's my question: obviously $ \left< A,B \right>_{\prime} = \frac{\pi}{1789} \mathrm{Tr}(A^{T}B)$ is a valid inner product as well! But this different choice of inner product would change the value of $\mathrm{Tr}(F)$!
I would have liked to think that $\mathrm{Tr}(F)$ is invariant under the choice of our inner product for some reason...since this is not the case, is the trace of a function like $F$ defined in terms the inner product $\left< A,B \right> = \mathrm{Tr}(B^{T}A)$? What's going on here?