very short 'time series' bulk rna-seq, testing two conditions
Hello, I have bulk rna-seq data that consist of two conditions (control, treated) tested across three time points (day 0, 1 and 3). We already observed by simple pair-wise (intra-condition) EdgeR that a big number of genes exhibit a change in expression between each two adjacent time points (day 1 vs 0 , then day 3 vs 1). We want to find significant differences INTER-conditions i.e genes whose change is significantly different in Treated vs Control at day 1 vs 0 , then day 3 vs 1. How could I do this with EdgeR? I have run EdgeR before but I do not know how to test both influence of treatment and time in one single design formula, and make sure that adjacent time points be tested (and NOT 3 vs 0 for exemple). I have 3 biological replicates by time-point and condition. Thanks for any help!
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