I have a time course RNAseq experiment with 2 different genotypes and 2 times (0h and 2h), there are 3 replicates each time
I am looking for a way to output genes that are degraded at 2h but not affected by the genotype condition. Meaning these genes can be strongly or weakly degraded at 2h, as long as the deregulation in A is equivalent to the deregulation in B, it is ok.
I have started a usual analysis of these data with DESeq2, so I've already output the results of the 2 Differential Expression analysis (2h VS 0h in condition A, and 2h VS 0h in condition B). I don't know if it is right to directly compare the FoldChange from both tables. Also, some genes do not have the same expression level at 0h. I was more thinking of making a new analysis using a design experiment like "~ genotype*time" and then using the altHypothesis with a FoldChange and pvalue thresholds but I am not sure how to set up this.
I am taking ideas.