I am getting started with DESeq2. I am trying to understand how multi-factor design works. This is fairly basic question, but I can't find the proper answer.
From the vignette:
So how exactly are the two parameters treated? What do the significant genes in the results mean? Are they the ones that are changing in condition regardless of type, or the ones that are changing in both type and condition? What happens when you have three or more parameters?
Additionally, although results for condition are output by default, results for type can be retrieved as well. Does the order or parameters only matter for the output or is the test performed differently?
From the vignette:
Code:
We can account for the different types of sequencing, and get a clearer picture of the differences attributable to the treatment. As condition is the variable of interest, we put it at the end of the formula. Here we design(dds) <- formula(~ type + condition) dds <- DESeq(dds)
Additionally, although results for condition are output by default, results for type can be retrieved as well. Does the order or parameters only matter for the output or is the test performed differently?
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