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!
Thank you very much, your answer is exactly what we need. I apologize for my late reply, we were testing the interaction in edgeR as you kindly suggested.
Thank you again, I didn't know I had to use "comment" to reply. Just a very last question, in DESeq2 is this also possible ?? (not very clear for me in DESeq2 vignette :( )
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions