You need to take into account that MATLAB operates column-wise by transposing your matrices:
>> a = [90,50;20,11;0,87;11,110]
>> b = [41,90;11,31;87,1;11,-2]
>> at = a.';
>> bt = b.';
>> xt = at==bt | at==bt([2,1],:)
>> at(xt)
ans =
90
11
87
11
This is your example data form your earlier comments. Please do not post the same question in multiple locations, it makes it vary hard for us to keep track of what information you have been given. Of course the examples you give here also work:
>> a = [1,2;3,4];
>> b = [2,5;3,0];
>> at = a.';
>> bt = b.';
>> xt = at==bt | at==bt([2,1],:);
>> at(xt)
ans =
2
3
Or using your method with a tolerance:
>> tf = abs(at-bt) < 1e-1 | abs(at-bt([2,1],:)) < 1e-1;
>> at(tf)
ans =
2
3
Note in all cases I used only the transposed matrices, because MATLAB operates columns-wise.
