Answers.Body: <p>This question was answered <a href="https://github.com/pachterlab/sleuth/issues/140" rel="nofollow noreferrer">here</a> </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-26T09:14:07.233Z
Answers.Text: Could you post here also the solution to your problem? Just to avoid having to chase the anser from site to site
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-26T00:10:53.477Z
Answers.LastActivityDate: 2017-09-26T00:10:53.477Z
Answers.UserDisplayName: elsoja
Body: <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.sstatic.net/ATPtp.png" rel="noreferrer"><img src="https://i.sstatic.net/ATPtp.png" alt="enter image description here"></a></p>
  
  <p><strong>Volcano plot (likelihood-ratio test q-values):</strong>
  <a href="https://i.sstatic.net/hovqx.png" rel="noreferrer"><img src="https://i.sstatic.net/hovqx.png" alt="enter image description here"></a></p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-15T17:17:05.727Z
Comments.Text: I’ve never used Sleuth but there are several odd things about this data as far as I’m concerned: the y-axis on the Wald test plot for instance seems way off (inflated). The q-values in the LR plot are a lot more reasonable.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-15T18:07:26.423Z
Comments.Text: Cross-posted [on biostars](https://www.biostars.org/p/267498/#267637) and the [kallisto mailing list](https://groups.google.com/forum/#!topic/kallisto-sleuth-users/bRb4nRhoZZw).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-15T19:53:11.537Z
Comments.Text: What does this look like if you plot Beta vs average TPM across all samples, excluding those with qval < 0.05?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-16T11:39:31.430Z
Comments.Text: What is the actual question? Why are some genes with beta = 0 and qvalue < 0.05?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-23T19:03:36.340Z
Comments.Text: Yes, that's the thing I can't understand
Comments.UserDisplayName: elsoja
Tags: <rna-seq><differential-expression>
Title: Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test
ThreadText: # Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test
  
  (Asked by: username_0 on 2017-08-15)
  
  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):**
  [![enter image description here](https://i.sstatic.net/ATPtp.png)](https://i.sstatic.net/ATPtp.png)
  
  **Volcano plot (likelihood-ratio test q-values):**
  [![enter image description here](https://i.sstatic.net/hovqx.png)](https://i.sstatic.net/hovqx.png)
  
  **Tags:** rna-seq, differential-expression
  
  > **Comments:**
  > **username_1**: I’ve never used Sleuth but there are several odd things about this data as far as I’m concerned: the y-axis on the Wald test plot for instance seems way off (inflated). The q-values in the LR plot are a lot more reasonable.  
  > **username_2**: Cross-posted [on biostars](https://www.biostars.org/p/267498/#267637) and the [kallisto mailing list](https://groups.google.com/forum/#!topic/kallisto-sleuth-users/bRb4nRhoZZw).  
  > **username_3**: What does this look like if you plot Beta vs average TPM across all samples, excluding those with qval < 0.05?  
  > **username_4**: What is the actual question? Why are some genes with beta = 0 and qvalue < 0.05?  
  > **username_0**: Yes, that's the thing I can't understand  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2017-09-26. Score: 1
  
  This question was answered [here](https://github.com/pachterlab/sleuth/issues/140)
  
  > **Comments:**
  > **username_4**: Could you post here also the solution to your problem? Just to avoid having to chase the anser from site to site  
  
  ---
  
  