[R] Get the difference between two matrices with different length

[Felix Wave]

Hello,
I have got two matrices with different length. The matrices have 3
columuns. The first two are coordinates. The third is a measurement.

Now I want to get a subtraction between every single value of the 
third column (between matrix1 and matrix2), but only if the two 
first coordinates in matrix1 and matrix2 are the same.

I tried "FUN=?" in aggregate and ave, but I don't know the command
for such a subtraction?


Thank's a lot.
Felix


---------------

The matrixes (examlple):

1 0.1 0.0042
1 0.2 0.00423
1 0.4 0.00467
1 0.5 0.00518
1 0.6 0.0061


1 0.1 0.0043
1 0.2 0.00442
1 0.3 0.00433
1 0.4 0.0045
1 0.5 0.00524
1 0.7 0.006



My aim:
-------
1 0.1 -0.0001
1 0.2 -0.00019
1 0.4 0.00017
1 0.5 -0.00006