Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test

Question

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):

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, Aug 15 '17 at 17:17
What does this look like if you plot Beta vs average TPM across all samples, excluding those with qval < 0.05? — gringer, Aug 15 '17 at 19:53
What is the actual question? Why are some genes with beta = 0 and qvalue < 0.05? — llrs, Sep 16 '17 at 11:39

score 1 · Answer 1 · answered Sep 26 '17 at 00:10

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answered Sep 26 '17 at 00:10

elsoja

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Could you post here also the solution to your problem? Just to avoid having to chase the anser from site to site – llrs Sep 26 '17 at 09:14

Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test

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