Does anyone know what the difference is between dispersion estimates obtained using
method="pooled" in the
estimateDispersions() function in DESeq? (I haven't migrated to DESeq2 yet; using DESeq 1.10.1.
From reading the vignette and reference manual, I get the impression that both of these methods estimate a single dispersion estimate for each gene, disregarding the particular experimental condition for each sample. But there must be other differences, why else have them as separate options? Looking at example code, it seems like
method="blind" goes together with
sharingMode="fit-only" (for DE analysis without replicates), but I wonder if that is a misinterpretation from my side.