Approaches for DESeq2 analysis with one factor and many levels
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fl ▴ 20
@fl-16173
Last seen 3 months ago
Germany

Hello,

I am interested in using DESeq2 to analyze a bulk RNA-seq dataset with one factor and 12 levels (control and treatments), and 4 biological replicates per level. I was wondering how using one or multiple input sample tables would influence the genes that are found to be differentially expressed. For example, 1) I could provide a single table of sample information and then look at the possible pairwise contrasts between control and treatment levels. Alternatively, 2) I could provide multiple sample tables, one for each control-treatment pair. Will there be major differences in the genes found to be differentially expressed between either approach for the same control-treatment comparison?

I would be grateful for any insights/suggestions.

deseq2 • 647 views
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@mikelove
Last seen 1 hour ago
United States

This is a FAQ in the DESeq2 vignette. 

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fl ▴ 20
@fl-16173
Last seen 3 months ago
Germany

Thank you, Michael.

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