The ANOVA procedure performs analysis of variance (ANOVA) for balanced data from a wide variety of experimental designs. In analysis of variance, a continuous response variable, known as a dependent variable, is measured under experimental conditions identified by classification variables, known as independent variables. The variation in the response is assumed to be due to effects in the classification, with random error accounting for the remaining variation.
The ANOVA procedure is one of several procedures available in SAS/STAT software for analysis of variance. The ANOVA procedure is designed to handle balanced data (that is, data with equal numbers of observations for every combination of the classification factors), whereas the GLM procedure can analyze both balanced and unbalanced data. Because PROC ANOVA takes into account the special structure of a balanced design, it is faster and uses less storage than PROC GLM for balanced data.
Use PROC ANOVA for the analysis of balanced data only, with the following exceptions: one-way analysis of variance, Latin square designs, certain partially balanced incomplete block designs, completely nested (hierarchical) designs, and designs with cell frequencies that are proportional to each other and are also proportional to the background population. These exceptions have designs in which the factors are all orthogonal to each other.
For further discussion, see Searle (1971, p. 138). PROC ANOVA works for designs with block diagonal matrices where the elements of each block all have the same value. The procedure partially tests this requirement by checking for equal cell means. However, this test is imperfect: some designs that cannot be analyzed correctly might pass the test, and designs that can be analyzed correctly might not pass. If your design does not pass the test, PROC ANOVA produces a warning message to tell you that the design is unbalanced and that the ANOVA analyses might not be valid; if your design is not one of the special cases described here, then you should use PROC GLM instead. Complete validation of designs is not performed in PROC ANOVA since this would require the whole matrix; if you’re unsure about the validity of PROC ANOVA for your design, you should use PROC GLM.