Question: why the p value and FDR is different between classic exactTest and glm glmQLFTest in edgeR?
0
gravatar for ZihaoXing
4 months ago by
ZihaoXing0
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?

edger • 154 views
ADD COMMENTlink modified 4 months ago by James W. MacDonald49k • written 4 months ago by ZihaoXing0
Answer: why the p value and FDR is different between classic exactTest and glm glmQLFTes
1
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald49k 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 4 months ago by James W. MacDonald49k

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

ADD REPLYlink written 4 months ago by Aaron Lun22k
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