Is it possible to specify random nested factor in DEseq2?
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yampolsk • 0
@194b0276
Last seen 4 weeks ago
United States

I would like to test differential gene expression in two groups of genotypes using genotypes nested within groups as a random effect. All genotypes measured in 2 treatments.

I understand that I can specify nested effect

dds <- DESeqDataSetFromMatrix(countData,
                              colData,
                              design= ~  treatment + group + group:treatment + group:genotype)

and this will test treatment and group as main effects and their interaction, but will group be tested against genotypes within groups?

Thanks!

nested DESeq2 • 142 views
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@mikelove
Last seen 1 hour ago
United States

I’d recommend to work out your statistical design with a local statistician or someone familiar with linear models in R. Unfortunately due to limits on my time I can only provide software-related support here.

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