This is a bit tricky. If you look at the help page for `DESeq`

, it says

```
sfType: either "ratio", "poscounts", or "iterate" for the type of
size factor estimation. See 'estimateSizeFactors' for
description.
```

And then if you do `?estimateSizeFactors`

you get this generic help page that is not useful at all. What you really need is the method help page, specifically for `DESeqDataSet`

objects. There's a way to get that using the `?`

operator, but I can't get it to work right now. You can always fall back on the `help`

function though. Using `help("estimateSizeFactors,DESeqDataSet-method", "DESeq2")`

(yes, I know, how would you ever figure out that you need that? By looking at the help pdf file, in particular the index page), you will get the correct help page, and it says this:

```
Usage:
## S4 method for signature 'DESeqDataSet'
estimateSizeFactors(
object,
type = c("ratio", "poscounts", "iterate"),
locfunc = stats::median,
geoMeans,
controlGenes,
normMatrix,
quiet = FALSE
)
Arguments:
object: a DESeqDataSet
type: Method for estimation: either "ratio", "poscounts", or
"iterate". "ratio" uses the standard median ratio method
introduced in DESeq. The size factor is the median ratio of
the sample over a "pseudosample": for each gene, the
geometric mean of all samples. "poscounts" and "iterate"
offer alternative estimators, which can be used even when all
genes contain a sample with a zero (a problem for the default
method, as the geometric mean becomes zero, and the ratio
undefined). The "poscounts" estimator deals with a gene with
some zeros, by calculating a modified geometric mean by
taking the n-th root of the product of the non-zero counts.
This evolved out of use cases with Paul McMurdie's phyloseq
package for metagenomic samples. The "iterate" estimator
iterates between estimating the dispersion with a design of
~1, and finding a size factor vector by numerically
optimizing the likelihood of the ~1 model.
```

Which I believe should answer your question.