Question

Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis?

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Sep • 0

@06de5a1f

Last seen 14 months ago

Germany

Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis? for example 7000 statistically significant genes out of 100000?

Thank you for your help.

DESeq2 • 818 views

ADD COMMENT • link updated 20 months ago by Michael Love 43k • written 20 months ago by Sep • 0

score 0 · Answer 1 · 2023-03-17

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Michael Love 43k

@mikelove

Last seen 6 hours ago

United States

Yes, this has been asked before on the support site, with paired analysis, you can have higher power.

Just look at plotCounts for representative genes.

ADD COMMENT • link 20 months ago Michael Love 43k

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Thank you for your reply.

I did the same, and I wanted to ask if the following plot make sense or I did sth wrong? The plot is for the gene with minimum padj value (<0.00001)

enter image description here

Thank you for your kind help in advance.

ADD REPLY • link 20 months ago Sep • 0

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Use group in ggplot to connect the pairs.

ADD REPLY • link 20 months ago Michael Love 43k