Hi Dan,

The assignment function is sizeFactors plus <-, so:

sizeFactors(dds) <- x

Then DESeq() will use these. This allows for customization and avoids
adding extra arguments.

Mike
On May 7, 2014 9:00 AM, "Schnell, Dan" <schnell.dj@pg.com> wrote:

> Hi,
>
> I would like to know if there is a way to specify Q75 be used for the
> locfunc in the estimateSizeFactors function of DESeq2 (instead of the
> default median).
>
> Calling estimateSizeFactorsForMatrix with locfunc=quantile does return
> sizeFactors based on min, Q25, median, Q75 and max, and one can then go
> through the normalizationFactors steps to do so, but it would be handy to
> know how to do this directly in the estimateSizeFactors function, or even
> the DESeq call itself.
>
> Thanks,
> Dan Schnell
>
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