Question about using LRT test for time course experiments with DESeq2
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Denise • 0
@860ad694
Last seen 8 hours ago
Spain

Hi,

I have an experimental design of treated versus control samples across 4 time points (A, B, C, and D) and I would like to use the LRT test to find compound-specific DE genes across these time points. However, I do not have a time point 0, meaning all 4 time points, consist of treated and control samples.

How can I use the LRT test to find DEGs for all time points including timepoint A?

Thank you, Denise

DESeq2 • 199 views
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@mikelove
Last seen 5 hours ago
United States

If you use the time series example in the workflow (rnaseqGene), you will get an effect for time point A and all the others. You would then use a LRT of ~condition + time + condition:time compared to a reduced design of ~condition.

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Hi Michael,

Thank you for getting back to me!

I am unsure if my question is very clear as I am new to this. I would like to use an LRT of compound + time + compound:time versus compound + time to capture compound-specific genes across time. I get the following coefficients

Intercept, compound_vs_CONTROL, timepoint_B_vs_A, timepoint_C_vs_A, timepoint_D_vs_A, compound.timepointB, compound.timepointC, and compound.timepointD

So there is no result for compound:timepointA! How can I get a coefficient/genes for this combination as well?

Thank you.

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I understood your question above (at least I think so) and my response above remains relevant.

How can I get a coefficient/genes for this combination as well?

I recommend to walk through the question and my response above with a local statistician or someone familiar with linear models in R.

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