[BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)

[Simon Anders]

Hi Dan

On 07.05.2014 15:00, Schnell, Dan wrote:
> Calling estimateSizeFactorsForMatrix with locfunc=quantile does
> return sizeFactors based on min, Q25, median, Q75 and max, and one
> can then go through the normalizationFactors [...]

This is because the 'locfunc' argument should be a function with one 
argument, but quantile takes to.

You should pass an anonymous function that calls 'quantile' with the 
second argument set to 0.75, as follows:

      dds <- estimateSizeFunctions( dds,
         locfunc = function(x) quantile( x, 0.75 ) )


   Simon