Question: Transcripts with beta close to zero are considered differentially expressed in a likelihood-ratio test in sleuth
0
gravatar for elsoja
2.5 years ago by
elsoja100
elsoja100 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 2.4 years ago • written 2.5 years ago by elsoja100

What sort of design do you have?

ADD REPLYlink written 2.5 years ago by Devon Ryan94k

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

ADD REPLYlink written 2.5 years ago by elsoja100

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

ADD REPLYlink written 2.5 years ago by Devon Ryan94k

They don't

enter image description here

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by elsoja100

I suspect you'll need to contact the authors.

ADD REPLYlink written 2.5 years ago by Devon Ryan94k

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

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

ADD REPLYlink written 2.5 years ago by elsoja100
1
gravatar for elsoja
2.4 years ago by
elsoja100
elsoja100 wrote:

This question was answered here

ADD COMMENTlink written 2.4 years ago by elsoja100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 644 users visited in the last hour