One-tailed test edgeR possible?

One-tailed test edgeR possible?

2

@2357cabb

Last seen 19 hours ago

Germany

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.


one-tailed


edgeR


DifferentialExpression


test

• 57 views

@james-w-macdonald-5106

Last seen 12 hours ago

United States

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.

@gordon-smyth

Last seen 21 minutes ago

WEHI, Melbourne, Australia

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.


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