Entering edit mode
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
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.
I understood your question above (at least I think so) and my response above remains relevant.
I recommend to walk through the question and my response above with a local statistician or someone familiar with linear models in R.