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I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
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That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
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You can take over some of the lines from `results()` to find them easily:
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Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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