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DESeq2 for one time-point versus two other time-points

Hello, I have three time-points with two replicates per time-point:

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After a confusing internet search, I'm at a loss. Is it possible to setup an overall comparison of Day2 versus Day4 and Day6? I'd like to avoid doing the individual comparisons of Day2 vs Day4, and Day2 vs Day6. Trying to compare one day versus two other days. If this is possible, how would I set this up? Thanks in advance!

deseq2
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written by jkanbar • jkanbar

Sure, simply add a column to that table called e.g. Factor which can be day2-day2-day46-day46-day46-day46 and then run the workflow with ~ Factor contrasting day2 to the Factor Day46 which then treats Day4 and Day6 as replicates. Alternatively, you can go with the contrast Day2 - ((Day4+Day6)/2) which would compare Day2 to the average of Day4 and Day6.

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written by ATpoint ATpoint

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