Hello, My setup looks like the following:
sample timepoint condition s1 0 plus s2 0 plus s3 0 minus s4 0 minus s5 1 plus s6 1 plus s7 1 minus s8 1 minus s9 2 plus s10 2 plus s11 2 minus s12 2 minus
I am trying to set up a DEXSeq DTU analysis. I am following this protocol: https://f1000research.com/articles/7-952/v3
So the model is going to be interaction between time and condition. How do I set this up using Dexseq, but at the DTU level? I am not sure what the full or reduced model will be.
Dexseq already requires an interaction term, which is condition:exon. I guess the interaction that I am interested in is condition and timepoint.
This is easier to do using DRIMSeq, as the full model will just have condition:timepoint, with the reduced model not having this interaction.
After thinking this through, I think the models will be:
formulaFullModel = ~ sample + exon + condition:exon + timepoint:exon+ condition:timepoint:exon formulaReducedModel = ~ sample + exon + condition:exon +timepoint:exon
However, I am wondering though, since we are comparing different isoforms, that the following reduced model makes more sense. Any thoughts?
formulaReducedModel = ~ sample + exon +timepoint:exon
For example, if the usage of an isoform goes from 30% to 40% to 50%, I think that baseline is also important.
Would appreciate if somebody could verify. Thanks in advance.