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  • Multiple comparisons using DESeq2

    I have a dataset with 4 time points: 3months, 6months, 1year, 2years and two conditions within each timepoint: WT and KO. I wish to find diff expressed genes between WT and KO from 3months to 6 months, 6 months to 1year, 1year to 2years, 3months to 2years, 3months to 1year, 6months to 2years. I used the design formula below:



    > coldata$Age_condition <- factor(paste0(coldata$Age, "-", coldata$condition))

    > dds <-DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~ Age_condition)

    > dds

    And got the following results:

    [1] "Intercept" "Age_condition1YR.KO"
    [3] "Age_condition1YR.WT" "Age_condition2YR.KO"
    [5] "Age_condition2YR.WT" "Age_condition3M.KO"
    [7] "Age_condition3M.WT" "Age_condition6M.KO"
    [9] "Age_condition6M.WT"

    How do I contrast to get the genes I want? This is where I am stuck. Thank you.

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