You need one column for each response variable and one column for each factor, with each row representing an observation. Regardless of whether factors are crossed or nested, use the same form for the data. Factor columns may be numeric, text, or date/time. If you wish to change the order in which text categories are processed from their default alphabetical order, you can define your own order. See Ordering Text Categories. You may include up to 50 response variables and up to 31 factors at one time.
Balanced data are required except for one-way designs. The requirement for balanced data extends to nested factors as well. Suppose A has 3 levels, and B is nested within A. If B has 4 levels within the first level of A, B must have 4 levels within the second and third levels of A. Minitab will tell you if you have unbalanced nesting. In addition, the subscripts used to indicate the 4 levels of B within each level of A must be the same. Thus, the four levels of B cannot be (1 2 3 4) in level 1 of A, (5 6 7 8) in level 2 of A, and (9 10 11 12) in level 3 of A.
If any response or factor column specified contains missing data, that entire observation (row) is excluded from all computations. The requirement that data be balanced must be preserved after missing data are omitted. If an observation is missing for one response variable, that row is eliminated for all responses. If you want to eliminate missing rows separately for each response, perform a separate ANOVA for each response.