Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test 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):
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