How many rows/columns can two-way ANOVA analyze?

With huge data sets, earlier versions of Prism 6 can crash or freeze while analyzing huge data tables with two-way ANOVA. Starting with Prism 6.07 and 6.0g, Prism doesn't freeze but says it can't do the analysis because there are too many rows or columns. 

How huge is huge? It depends on whether or not your data are repeated measures, but does not depend on which multiple comparisons tests you chose (if any).

No matching. Use regular two-way ANOVA (not repeated measures)

Prism will fail if:

 number of rows * number of columns > 16,384

Each column represents a different time point, so matched values are spread across a row

Prism will fail if:

(number of rows)^2 * number of columns * number of subcolumns * (number of columns + number of subcolumns) > 268,435,456

Each row represents a different time point, so matched values are stacked into a subcolumn

Prism will fail if:

number of rows * (number of columns)^2 * number of subcolumns * (number of rows + number of subcolumns) > 268,435,456

Repeated measures by both factors

Since Prism does not allow missing values in this case,  there are no special restrictions. If you can enter the data, Prism ought to analyze it.