<p>This question was answered <a href="https://github.com/pachterlab/sleuth/issues/140" rel="nofollow noreferrer">here</a> </p>

CC BY-SA 3.0
2017-09-26T09:14:07.233Z
Could you post here also the solution to your problem? Just to avoid having to chase the anser from site to site
llrs
CC BY-SA 3.0
2017-09-26T00:10:53.477Z
2017-09-26T00:10:53.477Z
elsoja
<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>

CC BY-SA 3.0
2017-08-15T17:17:05.727Z
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.
Konrad Rudolph
CC BY-SA 3.0
2017-08-15T18:07:26.423Z
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).
Devon Ryan
CC BY-SA 3.0
2017-08-15T19:53:11.537Z
What does this look like if you plot Beta vs average TPM across all samples, excluding those with qval < 0.05?
gringer
CC BY-SA 3.0
2017-09-16T11:39:31.430Z
What is the actual question? Why are some genes with beta = 0 and qvalue < 0.05?
llrs
CC BY-SA 3.0
2017-09-23T19:03:36.340Z
Yes, that's the thing I can't understand
elsoja
<rna-seq><differential-expression>
Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test
# 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  

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## 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  

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