**4.6k**wrote:

Does anyone know what the difference is between dispersion estimates obtained using `method="blind"`

vs `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.

**3.0k**• written 6.0 years ago by Mikael Huss ♦

**4.6k**

Maybe with pooled the dispersion derived via the regression is considered together with the higher evaluated dispersions caused by outliers (sharingMode="maximum" is usable) while with blind only the fit is considered (and only fit-only is a suitable choice for sharingMode)?

80Yes, maybe that's it. Thanks for the suggestion

4.6kI rapidly checked the code and there are some differences...apart from some checks about the existence of replicates with the pooled method. I will explore the code more deeply as soon as I can, but as a first try to clarify things I would like to visually compare dispersion plots derived with the two methods.

80Maybe it's something like the difference between the standard "pooled variance" (http://en.wikipedia.org/wiki/Pooled_variance) vs the "normal" variance. Thanks a lot for checking.

4.6kThe graphs are indeed different. If and when I manage to understand more about this issue I will report here. Thanks for the link!

80