Question: Significance of the interaction term in DESeq2
0
gravatar for cihan.erkut
4 months ago by
German Cancer Research Center, Heidelberg, Germany
cihan.erkut0 wrote:

Hi everyone,

I’m using DESeq2 to analyze RNA-Seq data. I have basically 2 factors: Genotype and Treatment. I build the design matrix as ~ Genotype * Treatment to capture interaction effects (Genotype:Treatment) as well. After correctly releveling the factors, I get the coefficients that I want. So far so good.

The question is, is there any way to test if the interaction term itself is significant? In more general terms, is there any way to create something like an ANOVA table on the DESeqResults object?

Cheers,

Cihan

deseq2 • 88 views
ADD COMMENTlink modified 4 months ago by Michael Love24k • written 4 months ago by cihan.erkut0
Answer: Significance of the interaction term in DESeq2
1
gravatar for Michael Love
4 months ago by
Michael Love24k
United States
Michael Love24k wrote:

Yes you can test the interaction term, see examples in ?results.

No, we do not build a series of results tables removing variables one by one from the end of the design.

ADD COMMENTlink written 4 months ago by Michael Love24k
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