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MAT TRANSFORM has two different forms:

MAT TRANSFORM <matrix file> BY <function of X#> 
transforms each element of the matrix according to <function of X#>.
For example to take natural logarithms of all elements of A, activate
MAT TRANSFORM A BY LOG(X#)
MAT TRANSFORM <X_matrix> BY <Y_matrix> AND <function of X#,Y#> 
transforms each element X# of <X_matrix> by <function of X#,Y#> 
where Y# is the corresponding element of <Y_matrix>.
For example, to divide each element of A by the corresponding element of
B, activate
MAT TRANSFORM A BY B AND X#/Y#

Besides current elements (X#,Y#), both forms of MAT TRANSFORM permit
referring to current row and column indices by I# and J#, respectively.
For example, a 10*10 matrix R of the form

        1   r   r^2 ... r^9
        r   1   r   ... r^8
        r^2 r   1   ... r^7
        ...         ...
        r^9 r^8 r^7     1

where r=1/2, can be created by MAT operations

   11 *                      r=1/2
   12 *MAT R=CON(10,10)
   13 *MAT TRANSFORM R BY r^abs(I#-J#)

  M = More information on MAT operations