DESeq2 on multiple sample groups
1
0
Entering edit mode
grsyhhsb • 0
@cdb4b488
Last seen 14 months ago
United States

Hello! I'm trying to run DESeq2 on samples that belong to different treatment groups. As an example:

                treatment_groups

Sample 1 responder to drug A

Sample 2 responder to drug A

Sample 3 non responder to drug A

Sample 4 non responder to drug A

Sample 5 responder to drug B

Sample 6 responder to drug B

Sample 7 non responder to drug B

Sample 8 non responder to drug B

I tried running DESeq2 on all the samples together and use results(dds, contrast=c("treatment_groups", "responder to drug A", "non responder to drug A")) to get the differential expression results for drug A response. I also tried just separating the samples and only have sample 1-4, which produced a somewhat different differential expression results. Is it recommended to do this one way or the other? Thanks in advance.

DESeq2 • 495 views
ADD COMMENT
1
Entering edit mode
swbarnes2 ★ 1.3k
@swbarnes2-14086
Last seen 16 hours ago
San Diego

In general, include all the samples you've got, to get better dispersion estimates and size normalization.

ADD COMMENT
0
Entering edit mode

I see. Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 738 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