Does it make sense to have so many statistically significant gene differentially expressed after DESeq2 paired sample analysis?
1
0
Entering edit mode
Sep • 0
@06de5a1f
Last seen 8 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 • 638 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 3 days 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
0
Entering edit mode

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
0
Entering edit mode

Use group in ggplot to connect the pairs.

ADD REPLY

Login before adding your answer.

Traffic: 455 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6