Let's consider $N$ different musical instruments. For each instruments, $k$ notes have been recorded at different frequencies. $M$ audio descriptors have been extracted from every instrument and every frequency. Therefore, for each frequency we have an $N\times M$ matrix:
$ A_1 = \begin{bmatrix} s_{11}^1 & s_{12}^1 & \dots \\ \vdots & \ddots\\ s_{N1}^1 & \dots & s_{NM}^1 \end{bmatrix} $
$ A_2 = \begin{bmatrix} s_{11}^2 & s_{12}^2 & \dots \\ \vdots & \ddots\\ s_{N1}^2 & \dots & s_{NM}^2 \end{bmatrix} $
$ \dots $
$ A_k = \begin{bmatrix} s_{11}^2 & s_{12}^k & \dots \\ \vdots & \ddots\\ s_{N1}^k & \dots & s_{NM}^k \end{bmatrix} $
and so on, where $s_{ij}^k$ means instrument $i$, descriptor $j$, frequency $k$.
1) I want to check if the differences between instruments remain constant at different frequencies. If they are not, I want to study how these differences change. What statistical tool should I use? Please note that I am not interested in how does an audio descriptor change at different frequencies, but whether different instruments change homogeneously.
2) Suppose that the $N$ instruments can be grouped into 3 different classes (e.g. instruments from 1 to 5 belong to class 1, instruments from 6 to 20 belong to class 2 and so on). How can I take this grouping into account? For example, how can I check if the differences within a group are more constant wrt differences between different groups?
EDIT: I have been suggested to use multi-level regression analysis, which seems suitable for this case, but I am a bit confused: what is the variable to be predicted in this case? How can I use this technique?