We often write matrices as $A=(a_{ij})$. But what do the subscripts mean? Does it simply say that $A$ is a $2$-dimensional array?
I read somewhere in the definition of the transpose of a matrix that if $A=(a_{ij})$ then its transpose is $A^T=(a_{ji})$. I had a problem with this. By $(a_{ij})$ it is understood that we are talking about the matrix $\begin{bmatrix}a_{11}&a_{12}&...&a_{1n}\\a_{21}&a_{22}&...&a_{2n}\\...&...&...&...\\...&...&...&...\\a_{m1}&a_{m2}&...&a_{mn}\end{bmatrix}$.
Then $(a_{ji}),(a_{mn}),(a_{pq})$ should all stand for the same matrix (the one above).
Could someone explain to me the meaning of the notation or provide a better one?
The first subscript, usually $i$, stands for the row index. The second one stands for the column index.
The point when writing $A^T=(a_{ji})$ is that $i$ and $j$ are not really dummy variables here as you seem to imply: what is meant is really
$a_{ji}$ is the entry at the intersection of the $j$-th row and the $i$-th column of $A$ (you know that because here $j$ comes first), and it is meant to become the entry at the intersection of the $i$-th row and the $j$-th column in $A^T$ (you know that because in $b_{ij}$, $i$ comes first).