I'm comparing the results that I obtain when doing a DE analysis with the Wald test and the likelihood-ratio test. One the thing that I've noticed is that there are many genes with 'beta' close to zero that are considered differentially expressed between the conditions.

I know that the likelihood-ratio test does't use the beta values to calculate the p-values, but I find it strange that transcripts with similar expression values between the conditions are being considered differentially expressed.

**Volcano plot (Wald test q-values):**

**Volcano plot (likelihood-ratio test q-values):**

What sort of design do you have?

It's a simple design with just one condition: Tissue A (6 samples) vs. Tissue B (3 samples)

I wonder if the plots would look similar if you changed the y-axis of the Wald-test results.

They don't

I suspect you'll need to contact the authors.

I've done this already. Waiting for an answer. Thank you!

https://groups.google.com/forum/#!topic/kallisto-sleuth-users/bRb4nRhoZZw