DESeq2 : Using contrast in results vs performing complete independent analysis
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@andree-anne-20906
Last seen 12 weeks ago
Canada

Hi

I have a question regarding different results when using contrast in DESeq2 vs when I do the analysis separately.

I have 3 groups : A : condition A; n = 25 B : condition B; n = 25 C : controls; n = 350

I first looked at differently expressed genes between A and C, and B and C separately. I performed the analysis and then retrieve the separate results for each analysis using contrast.

However, if I use contrast to compare A and B, (when C is considered in the dispersion analysis) vs performing an isolated analysis for A and B, the results are not the same. (no FDR genes with the first approach vs plenty with the second)

I am wondering if the number of controls "masks" the difference I could identify between A and B when it is considered in the dispersion.

In this case, I am wondering if performing an independent analysis for A an B is better.

Many thanks !

DESeq2 • 177 views
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@mikelove
Last seen 14 hours ago
United States

This is answered in the vignette FAQ.

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