Hi everyone,

I know related questions about this topic has been asked, but I still have an important doubt about the difference of interpretation of DESeq2 if it is used with Wald test or with Likelihood Ratio Test . (I also asked few days ago a very complex question, but this time i can be more concise).

Provided that Wad test and LRT are two different tests, the p-value obtained has two different interpretations. However, in 2 condition's comparison they bring similar results. Furthermore, if instead of 1 v 1 comparison, we have more than 2 class, and we want to conduct pairwise comparisons, how will be the interpretation of the p-value be in case of LRT? Since the way of assigning p-value will depend on the comparison of the full model against the model without "condition" and "condition" will have 4 class, I cannot clearly see how can i interpret p-value, and if it is valid and appropriate to use LRT if pairwise comparison are wanted to be conducted. Will the interpretation in that case be bias because it is summed up as "if it is found to be significant in ANY class, then the p-value will be significant"? Will in that case work anyways as I am also considering Genes significant by log2foldchange threshold as well?

Thanks for your time, any comment on that will be super welcomed!

Eric.