DESeq2 on multiple sample groups
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grsyhhsb • 0
@cdb4b488
Last seen 22 days 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 • 118 views
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swbarnes2 ★ 1.2k
@swbarnes2-14086
Last seen 30 minutes ago
San Diego

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

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I see. Thank you!