Question: Transcripts with beta close to zero are considered differentially expressed in a likelihood-ratio test in sleuth
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gravatar for elsoja
2.2 years ago by
elsoja70
elsoja70 wrote:

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

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

enter image description here

ADD COMMENTlink modified 2.1 years ago • written 2.2 years ago by elsoja70

What sort of design do you have?

ADD REPLYlink written 2.2 years ago by Devon Ryan92k

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

ADD REPLYlink written 2.2 years ago by elsoja70

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

ADD REPLYlink written 2.2 years ago by Devon Ryan92k

They don't

enter image description here

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by elsoja70

I suspect you'll need to contact the authors.

ADD REPLYlink written 2.2 years ago by Devon Ryan92k

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

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

ADD REPLYlink written 2.2 years ago by elsoja70
1
gravatar for elsoja
2.1 years ago by
elsoja70
elsoja70 wrote:

This question was answered here

ADD COMMENTlink written 2.1 years ago by elsoja70
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