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edgeR functions do not do any filtering, i.e., they do not remove any genes from the results or from the plots. The only filtering was that which you did explicitly yourself by: keep <- filterByExpr(R10LB_0vs0.5) R10LB_0vs0.5_filter <- R10LB_0vs0.5[keep, keep.lib.sizes = FALSE] For your data, filterByExpr will keep any gene that is expressed at a ...


DE results do not change from one run to another. The code given in your question will give identical results each time you run it.

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