If the data set is large and a few random points are missing the problem is not serious, yet in a smaller data set with a non-random distribution of missing values the problem may be serious.
Deletion is often the default option with statistical software packages.
Estimates may be made upon, prior knowledge, inserting mean values, and using regression. The matrix is computed using only values which are common to both variables, ie. In sociological studies it is potentially the case that a failure to respond may be indicative of some form of behavior.