Hello ! PhD student and working with rna-seq data, I used DESeq2 for my analysis but after finishing my work, I believe some elements were misunderstood when using the software. To explain I summarized my model analysis: 3 genotypes (G1,G2,G3) in 3 conditions (T1,T2,T3) and my model: I'm interesting by the effect of genotype and treatment but especially by the interaction term in my work. So the design appropriated seem to be:
design = formula(~G + B + G:B)
Reference factors are : G1 and T1
intercept : base mean of G1 in T1 (reference) G2vsG1 : Genotype 2 against reference G1 in T1 G3vsG1 : Genotype 3 against reference G1 in T1 T2vsT1 : treatment 2 against treatment 1 in T1 T3vsT1 : treatment 3 against treatment 1 in T1 G2:T2 : treatment 2 effect in G2 G3:T2 : treatment 3 effect in G2 G2:T3 : treatment 2 effect in G3 G3:T3 : treatment 3 effect in G3
The model built with every parameter compared to the references. following the DESeq2 vignette I built the contrast test for example :
effect of the T2 compare to the T1 for G1 (treatment 2 effect on the genotype 1) :
effect of the T2 for G2 compared to G1 (treatment 2 effect on the genotype 2):
effect of the T2 for G2 against G3 (treatment 2 effect and genotype 2 vs genotype 3 effect = genotype environment interaction):
If I understood, for the last example, I tested the GxE effect in the treatment 2 corrected by the treatment 1 (the reference) and compared between 2 genotypes (typically as in a linear model in R).
After that, I have some contrast files, especially with log2foldchange but I didn't understand the underlying comparison. If I want to test the effect in a genotype of the treatment 2 against 1 it's the ratio between the two treatment (with the fact that there is some modifications by deseq with shrink etc. not simply the ratio but the idea is here). But the logfoldchange for my last example when I test GxE is not clear and Deseq2 help and forum did'nt gave me an information about. Is it a ration between genotype in the treatment 2 after correction for the treatment 1 ? a ratio of ratio ?