I am having some doubts when trying to extract relevant info from my gene lists generated by LRT in DEseq2.
Now I have gene lists of differentially expressed genes explained by:
- the interaction of the 2 conditions that were applied to my cells,
- condition 1
- and condition 2
I have been trying to explore this data, by splitting the lists into Up and Down-reg gene lists, and entering these signif genes to GO in R, Panther and GOrilla, for example. Nevertheless, I have several levels per each condition, and I am not convinced that I am interpreting the results properly:
The reference condition in LRT is not the reference condition anymore, right? I am comparing the full design with the reduced design, not experimental conditions vs a reference condition. To do that I should do Wald, right? And from Wald, extract Up/Downs. But then I need to run many, many contrasts (more than 0).. and I don't feel this is how I should be doing this.
Is it correct to explore and visualize UP/DOWNs from the LRT gene lists? Or does it makes more sense to just say "these genes are affected by the interaction of condition1 and condition2 (LRT p.adj)", but then I have to run Wald to explain when are these genes up/down regulated?
I was also trying to plot my results in a heatmap where I could see the top diff. expressed genes for all the different conditions, but then is where I realize that the comparison is not against a reference anymore, but against the full model, so a heatmap would make no sense in this case. May I ask what would be the best way to visualize this result?
Thank you for your time, once again.