I tried to look the documentation for interaction.But, Unable to understand difference between groups and interaction.So difference between following codes, Is it basically same, different ways of doing it?
dds$group <- factor(paste0(dds$race, dds$sampletype))
design(dds) <- ~ group
design(dds) <- ~ genotype + condition + genotype:condition
I have this coldata, miRNA expression for ( sampletype(normal and cancer), ER status, her2 status). I want to get one table of results for ER status (positive vs negative ) compared to sampletype and another table by Her2 status compared to sample type.
So my question here is, do I have to have dds twice? of I can produce one dds and then compare later?
basically i have three variables, all examples are based on two.