Is it possible to conduct a one-tailed differential expression analysis test using edgeR? I might have missed something in the documentation, but I cannot find anything definite.
I mean by this conducting a test where I only look for over expression in one sample group, but not in the other.
No, we don't provide one-sided tests in edgeR because we don't recommend them.
If you compare two groups which have roughly the same number of replicates and sequencing depth, then the one-sided p-value would just be half the two-sided p-value for genes where the logFC is in the same direction as the alternative hypothesis.
I don't believe it's possible to do so using edgeR, as neither a likelihood ratio test nor an F-test provides directional testing like that. You could use limma-voom or limma-trend and then simply re-calculate the p-values using pt with the correct argument for lower.tail, depending on the directionality of your comparison.
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version 2.3.6
In limma, the one-sided p-value is just half the two-sided p-value for genes where the logFC is in the same direction as the alternative hypothesis.
Well yes, but that doesn't preclude one from using the Excel methodology of taking half the p-value and calling it a day.
Yes, that's what I'm saying. I was agreeing with your answer, just adding that it isn't necessary to rerun
pt.