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  • DESEq2 Paired samples: Baseline Versus each Timepoint

    I am a newbie and I have the following experimental factors as below. I read very carefully the different posts and tutorial but I am still uncertain on how to design my experiment formula.

    I wanted to know how to use DSEQ2 to look at the paired samples to see which genes are being differentially expressed when compared to Baseline eg:

    Q1) Baseline Vs Day1: list of DE genes

    Q2) Baseline Vs Day2: list of DE genes

    Q3) Baseline Vs Day3: list of DE genes



    eg: design(dds)=~ Patient.ID + Timepoint

    Is that right ??? How do you get the DE list of genes for each Q1-Q3 above ??
    Can Someone please help ?

    Thank you in advance

    Code:
    >df
     Patient.ID library Timepoint
    1           1       A  Baseline
    2           1       A      Day1
    3           1       A      Day2
    4           1       A      Day3
    5           2       A  Baseline
    6           2       A      Day1
    7           2       A      Day2
    8           2       A      Day3
    9           4       A  Baseline
    10          4       A      Day1
    11          4       A      Day2
    12          4       A      Day3
    13          5       B  Baseline
    14          5       B      Day1
    15          5       B      Day2
    16          5       B      Day3
    17         10       B  Baseline
    18         10       B      Day1
    19         10       B      Day2
    20         10       B      Day3
    21         11       B  Baseline
    22         11       B      Day1
    23         11       B      Day2
    24         11       B      Day3
    25         13       C  Baseline
    26         13       C      Day1
    27         13       C      Day2
    28         13       C      Day3
    29         17       C  Baseline
    30         17       C      Day1
    31         17       C      Day2
    32         17       C      Day3
    33         18       C  Baseline
    34         18       C      Day1
    35         18       C      Day2
    36         18       C      Day3

  • #2
    The design formula looks correct. To get the DE results as requested, the syntax is:

    Code:
    result_day1<-results(dds,contrast=c("Timepoint","Day1","Baseline"))

    Comment

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