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  • Multi group comparisons in baySeq

    I am having trouble setting up the group model structure to test on my data(consists of 3 replicate samples for each of 4 treatments/groups).

    I want to test the following models:
    no differential expression(NDE)
    pairwise comparisons of treatment groups for DE:
    1 vs (2,3,4) 2 vs 3 2 vs 4 3 vs 4

    I have completed the analysis for NDE and DE for [1 vs (2,3,4)].
    Here is the replicate and model structure code I used:
    replicates=c(1,1,1,2,2,2,3,3,3,4,4,4)
    groups=list(NDE=c(1,1,1,1,1,1,1,1,1,1,1,1),DECvS=c(1,1,1,2,2,2,2,2,2,2,2,2))

    Q1) If I use the following model structure as an example, what DE genes am I getting (FDR 10%)? Those that are different between groups 1,3 and 2,4, and also different between groups 2 and 4?
    replicates=c(1,1,1,2,2,2,3,3,3,4,4,4)
    groups=list(DEHvST=c(0,0,0,1,1,1,0,0,0,2,2,2))

    Q2) I need help coding the proper model structure to make pairwise comparisons where I only want to focus on two groups at a time (2 vs 3 2 vs 4 3 vs 4), replicate structure = (replicates=c(1,1,1,2,2,2,3,3,3,4,4,4))

    Any suggestions would be greatly appreciated!!

    Thanks,
    Laramy

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