The fact you're getting an error shows that you're using an older version of matlab. In R2016b and later, there would have been no error (but the result may not have been what you've wanted).
If the result is supposed to be a 2000 x 2000 matrix of the difference of the cartesian pairs from the two vectors:
E = bsxfun(@minus, ecg, y);
This is the result you'd get from newer versions of matlab.
If the result is suppose to be the difference of the two vectors regardless of their shape, then first you need to take a good look at your code and ask why aren't these two vectors both row vectors or both column vectors. The best way to solve your problem would be to change whatever created one of them so they're both the same shape. Alternatively,
E = ecg - y.';
But really fix your algorithm. These vectors should not be in different directions.
