Hi,

I've read the instruction for performing likelihood ratio test. The example is clear but in the test dataset there are only two conditions (wildtype and mutant).

I have dataset with data for four maize lines two tissues and 12 time-points. I wonder if it is possible to make pairwise comparisons using full dataset.

Or should I

1. Compute size-factors for full DESeqDataSet and use formula ~line + time + line*time (comparisons across tissues are not of interest)
2. Subset the full dataset to contain only one tissue and two lines and compare them.
3. Repeat step 2. for each pairwise comparison within each tissue
4. Do FDR correction for all p-values ?

Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make comparisons you care about using Wald statistics. The LRT is meant as an omnibus test to determine if a larger model fits better than a reduced model, and is not really applicable to what you are trying to do.