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Old 11-05-2015, 03:31 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

For the question of, "What genes change over time?", what you want to do is an LRT test where the reduced model lacks the time component. This will give you everything that changes, regardless of whether it's a consistent change or only up/down at one time point.

Other than that, I think people are typically encouraged to spend some time with the PCA plots. You can often make some guess as to useful pairwise comparisons from them.

Edit: Note that fold changes from the LRT results probably aren't meaningful, but the p-values are.
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