Strassen algorithm for matrix multiplication complexity analysis
It's true that the parameter $n$ usually denotes the size of the input, but this is not always the case. For square matrix multiplication, $n$ denotes the number of rows (or columns). For graphs, $n$ often denotes the number of vertices, and $m$ the number of edges. For algorithms on Boolean functions, $n$ denotes the number of inputs, though the truth table itself has size $2^n$. There are many other examples.