lsmeans, I'm testing the pairwise comparisons among factor1 levels for each different combination of factor2 and factor3 levels:
(model was produced by
The last line in the output states:
P value adjustment: holm method for 3 tests
It seems that lsmeans corrects MCP only within each combination of factor2 and factor3, but not across the combinations (In my data there are 14 combinations of factor2 and factor3 and 3 levels within factor1, so the number of total tests is 42).
- Is this behavior reasonable? Doesn't it inflate the overall type I error? Why is this the default?
- How can one make lsmeans correct across combinations (i.e. for the total number of tests?)