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Answer: collapseReplicates error after tximeta
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The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
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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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Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
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