Question: why the p value and FDR is different between classic exactTest and glm glmQLFTest in edgeR?
gravatar for ZihaoXing
8 weeks ago by
ZihaoXing0 wrote:

i found the the p value and FDR are lower using exactTest than using glmQLFTest in edgeR when comparing two groups , I want to know why the results is very different between exactTest and glmQLFTest?

ADD COMMENTlink modified 8 weeks ago by James W. MacDonald48k • written 8 weeks ago by ZihaoXing0
gravatar for James W. MacDonald
8 weeks ago by
United States
James W. MacDonald48k wrote:

Because they are different tests that make different assumptions about the underlying data. The exact test is similar to an exact binomial test, but allowing for over-dispersion. The glmQLFTest uses a quasi-likelihood F-test that incorporates uncertainty in the count estimation. The help pages for both functions have citations that you can read if you care to know more.

ADD COMMENTlink written 8 weeks ago by James W. MacDonald48k

And also, glmQLFTest is better in every respect and should be the method of choice.

ADD REPLYlink written 8 weeks ago by Aaron Lun21k
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