Question

DESEQ experimental design

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edu.hsv.crs • 0

@eduhsvcrs-17028

Last seen 6.4 years ago

I have two replicates for each time points(0,2h,4h). How to design an experiment with deseq2.

deseq2 • 961 views

ADD COMMENT • link updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by edu.hsv.crs • 0

score 0 · Answer 1 · 2018-08-23

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Michael Love 43k

@mikelove

Last seen 6 days ago

United States

And you want to find genes that change at either time point relative to 0hr?

ADD COMMENT • link 6.4 years ago Michael Love 43k

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Hi Michael,

Yes, I want to find out genes that change at either time point relative to 0hrs.

ADD REPLY • link 6.3 years ago edu.hsv.crs • 0

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You can use a likelihood ratio test, you would use a design of ~time, and then:

dds <- DESeq(dds, reduced=~1, test="LRT")
res <- results(dds)

See the LRT section of the vignette, and read over ?results for some more details.

ADD REPLY • link 6.3 years ago Michael Love 43k

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Nevermind, I just saw your reply there!!

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Hi Michael, I have a similar question that I posted at: C: Using the "listValues" argument of DESEQ in multiple group comparisons yesterday

Not sure if you got a notification for that, I was wondering if you could help me out with that?

ADD REPLY • link 6.3 years ago Ashu ▴ 10

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Thank you Michael! I have another question. If treatments are imparted at different time points, what would be the design?

ADD REPLY • link 6.3 years ago edu.hsv.crs • 0