Update: I have attached to mat files. I want to compare the rows in file A to that of file B. If a number in the first column of B matches with that of a number in the first column of A, then the entire row in A in which the number matches with that in B should be deleted. So example if you look at file B, the number 12 is in column 1, row 2 and it matches with column 1, row 4 in A. In this case I want a code that will delete the entire row 4 in A. I will now be left with 6by4 matrix. I am trying to compare the headers and use it as a quide to remove rows in A that I dont want. I have a very large data set and having a code that can do this will be very helpful.