I think this question may have been already asked before, but I have not been able to find an answer, or I did not fully understand the answers, as I'm a beginner in DE analysis.
Considering the following RNAseq dataseq, imported in DEseq2 : 12 samples, with 2 conditions, and 3 replicates fore each combination of conditions
NT: normal temperature
ST : stress temperature
NW : normal watering
SW : stress watering
> colData(dds) temperature watering <factor> <factor> sample1.1 NT NW sample1.1 NT NW sample1.1 NT NW sample2.1 NT SW sample2.2 NT SW sample2.3 NT SW sample3.1 ST NW sample3.2 ST NW sample3.3 ST NW sample4.1 ST SW sample4.2 ST SW sample4.3 ST SW
I would like to do a "all vs all" comparison between all the groups of replicates,but i'm not really sure what design should I use for that.
By this I mean that I would like to have a list of all genes that are differentially expressed between all combination of conditions NT/NW, NT/SW, ST/NW, ST/SW. (sample1 vs sample2, sample 1 vs sample3, sample1 vs sample 4, sample 2 vs sample 3 ... etc... )
Thanks for any of your input.