DESEq2 Paired samples: Baseline Versus each Timepoint

[David Lyon]

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

>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

[retropc]

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

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