I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the interaction between two variables, one (INJ) with two conditions (L,S) and the other (SOC) with four conditions (A,B,C,D). We also have a third variable for tissue type (TIS) from 3 tissues (H,N,T), although we are not interested in this variable for this particular question.
We were able extract DE genes underlying the interaction of interest in DESeq2 using an LRT test. We also ran WGCNA to get gene clusters and looked at trait correlations. Using these WGNCA clusters and VST normalized count data, I would like to run GSEA or a similar analysis to find WGCNCA clusters that differ based on the interaction between the two main variables.
What I've tried so far was generating a pseudo-variable that is a combination of INJ and SOC with 8 separate conditions for running in GSEA, but this doesn't quite get at the interaction between variables since we really want to see if the effect of INJ differs between SOC conditions.
One thing I was thinking was running a GSEA-like analysis on log2 ratios between INJ states for each SOC condition, but these would have to be summary statistics for groups of samples and I would lose the variance of expression within groups (maybe that doesn't matter though for exploratory analysis?). This would also reduce my "sample" count to 1 per condition, which isn't ideal for this type of analysis and I would probably have to look at differences between gene sets instead of phenotypes for more robust stats.
Any thoughts on ways to do this? I don't need to use GSEA if there is another analysis I could run on gene sets that allows for more complex experimental models. Thanks in advance.