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Transcripts with beta close to zero are considered differentially expressed in a likelihood-ratio test in sleuth

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

sleuth rna-seq differential-expression
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written by Antonio Camargo Antonio Camargo

What sort of design do you have?

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written by Devon Ryan Devon Ryan

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

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written by Antonio Camargo Antonio Camargo

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

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written by Devon Ryan Devon Ryan

I suspect you'll need to contact the authors.

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written by Devon Ryan Devon Ryan

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written by Antonio Camargo Antonio Camargo

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