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Hi, guys! I have a question about how to make the contrast in DESeq2. I have RNA-seq samples. They are from patients treated with two drugs and collected at two-time points. I want to find some genes with significant expression changes in two-time points between two drugs.
Patient | Drug | Time|
P1 | A | Day 0
P2 | A | Day 0
P3 | A | Day 0
P4 | B | Day 0
P5 | B | Day 0
P6 | B | Day 0
P1 | A | Day 1
P2 | A | Day 1
P3 | A | Day 1
P4 | B | Day 1
P5 | B | Day 1
P6 | B | Day 1
The contrast I want: ( Patients on Day1 of DrugA - Paired patients on Day0 of DrugA) -( Patients on Day1 of DrugB - Paired patients on Day0 of DrugB).
- I don't know how to achieve the contrast that I want in DESeq2 or other expression analysis algorithms like limma, or edgeR. Please give me some advice! Thanks!
