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
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
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