Best method for differential expressed genes between 3 environmental observations
I have three groups of environmental RNA- Seq data (5-6 replicates each) and would like to see the differential expressed genes between them (ie: genes that are DE in L1, in L2 and in L3). I have seen many statistical methods use a control to compare to, but I don't have control since I am comparing environmental data; and tests between only two groups, where I have 3. What would be your best recommendation. I have 3 observations (5-6 replicates each) and about 5000 genes.
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Compare L1 vs L2, L1 vs L3 and L2 vs L3, that are the pairwise comparisons you can make. All of the tagged tools support that.