Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis?
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@06de5a1f
Last seen 6 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 • 525 views
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@mikelove
Last seen 19 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.

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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.

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Use group in ggplot to connect the pairs.

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