I’ve been searching for answers to this for awhile now. DESeq2 in R seems (I think) to have the ability to input a 2x2 factorial design and retrieve differentially expressed genes significant by interaction. I can’t seem to figure out how to perform that in Galaxy though. If any has a tutorial or tips please let me know. Below is what I have tried so far.
My experiment is setup as follows:
I have tried defining the following:
Factor 1 as Healthy vs Disease with:
Healthy as Factor Level 1 and Disease as Factor Level 2
Factor 2 as Vehicle vs Drug with:
Vehicle as Factor Level 1 and Drug as Factor Level 2
When I run it in galaxy, I define all healthy samples (both healthy + vehicle and healthy + drug) as part of Factor 1 - Factor Level 1; all diseases samples (both disease + vehicle and disease + drug) as part of Factor 1 - Factor Level 2; all vehicle samples (both healthy + vehicle and disease + vehicle) as part of Factor 2 - Factor Level 1; and all vehicle sample (both healthy + drug and disease + drug) as part of Factor 2 - Factor Level 2.
I only ever get differentially expressed genes between the Healthy and Disease - none of the individual pairwise comparisons or the interaction term like you would in a 2-way ANOVA?
Does anyone have a method for obtaining this or a tutorial that I could refer to? Any help would be really appreciated!