dispersion and variability of samples/replicates in DESeq2
I am a bit confused about the definitions of "replicates" and "samples".
DESeq2: The starting point of a DESeq2 analysis is a count matrix K with one row for each gene i and one column for each sample j. Within-group variability, i.e., the variability between replicates, is modeled by the dispersion parameter α i, which describes the variance of counts via VarKij=μij+αiμ2ijVarKijμijαiμij2.
Can I also say that dispersion models the variability between the samples? Does "replicates" and "samples" mean the same object here? Why would one call "samples" as "replicates" and vice versa? If yes, what is "within-group variability", namely why is it called "within-group"?
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