text: user1334: 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):
  
  
  user1334: This question was answered here 
  
original_text: 1334: <p>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.</p>
  
  <p>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.</p>
  
  <p><strong>Volcano plot (Wald test q-values):</strong>
  <a href="https://i.stack.imgur.com/ATPtp.png" rel="noreferrer"><img src="https://i.stack.imgur.com/ATPtp.png" alt="enter image description here"></a></p>
  
  <p><strong>Volcano plot (likelihood-ratio test q-values):</strong>
  <a href="https://i.stack.imgur.com/hovqx.png" rel="noreferrer"><img src="https://i.stack.imgur.com/hovqx.png" alt="enter image description here"></a></p>
   1334: <p>This question was answered <a href="https://github.com/pachterlab/sleuth/issues/140" rel="nofollow noreferrer">here</a> </p>
  