Question

DESeq Timepoint Design (using Baseline as reference)

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ez935 • 0

@ez935-15961

Last seen 5.9 years ago

Hi,

I'm using DESeq2 to perform differential analysis on RNA-Seq data for three different timepoints (Baseline, Acute, Severe).

I've looked at differential genes for pairwise comparisons between timepoints: Acute vs. Baseline, Severe vs. Acute, and Severe vs. Baseline.

How would I make a design to test if genes from Severe vs. Baseline are different from Acute vs. Baseline ?

Thank you in advance!

deseq2 • 590 views

ADD COMMENT • link updated 5.9 years ago by Michael Love 41k • written 5.9 years ago by ez935 • 0

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Are you trying to identify specific genes that have different response in the two conditions, or are you just trying to determine whether the two gene signatures are distinct?

ADD REPLY • link 5.9 years ago Ryan C. Thompson ★ 7.9k

score 0 · Answer 1 · 2018-05-30

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Michael Love 41k

@mikelove

Last seen 1 day ago

United States

See this related question:

A: [DESeq2] Difference between results from using contrast option and using name op

ADD COMMENT • link 5.9 years ago Michael Love 41k