DESeq2 about comparasion of gene expression change on two-time points between two group samples.
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simon • 0
Last seen 13 months ago
Hong Kong

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).

  1. 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!
DESeq2 RNASeqData edgeR limma DifferentialExpression • 674 views
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swbarnes2 ★ 1.4k
Last seen 1 day ago
San Diego

Look up 'interactions' in the DESeq2 vignette


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