Thanks very much to both of you for the 2 simpler solutions--I really appreciate it. Dan Schnell ------------------------------ Message: 7 Date: Wed, 07 May 2014 15:45:06 +0200 From: Simon Anders < > To: bioconductor at r-project.org Subject: Re: [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love) Message-ID: <536A38E2.8010407 at embl.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed 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