How to represent a 2-D data matrix in a database

RDBMSes aren’t flat. The R part sees to that. What you need is:

Table Entity
------------
ID

Table EntityData
----------------
EntityID
MatrixRow (1, 2, 3...)
MatrixColumn (A, B, C, D...)
Value

Entity:EntityData is a one-to-many relationship; each cell in the matrix has an EntityData row.

Now you have a schema that can be analyzed at the SQL level, instead of just being a data dump where you have to pull and extract everything at the application level in order to find out anything about it.