multiple group comparison
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@capricygcapricyg-17892
Last seen 21 months ago
United States

Hello, DESeq2 users,

I recently worked on differential expression analysis for a dataset containing 3 different treatments (A, B, and C). I called about 600 DE genes between group A and group C, 1 DE gene between A and B, and 0 DE gene between B and C.

I really would like to get some help about data interpretation here. Since groups A and B were so similar and A and C were different in about 600 genes, I expected that at least some hundreds of DE would be called between groups B and C. How do I get 0 between B and C here?

Thank you so much for your help.

C.

deseq2 • 423 views
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@mikelove
Last seen 2 hours ago
United States

This can happen for many reasons and doesn’t indicate any issue with how you’ve run the code. You may want to look at a PCA plot to get a sense of the samples.

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I have to say samples are not clustered very well on PCA plot...

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