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

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Schnell, Dan ▴ 30

@schnell-dan-6540

Last seen 9.6 years ago

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 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.0 years ago by Simon Anders ★ 3.7k • written 10.0 years ago by Schnell, Dan ▴ 30

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Michael Love 41k

@mikelove

Last seen 13 hours ago

United States

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD COMMENT • link 10.0 years ago Michael Love 41k

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Thanks very much Michael, for your efficient solution and quick response. Dan Schnell From: Michael Love [mailto:michaelisaiahlove@gmail.com] Sent: Wednesday, May 07, 2014 9:11 AM To: Schnell, Dan Cc: bioconductor@r-project.org Subject: Re: [BioC] How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love) 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<mailto: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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD REPLY • link 10.0 years ago Schnell, Dan ▴ 30

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Simon Anders ★ 3.7k

@simon-anders-3855

Last seen 3.7 years ago

Zentrum für Molekularbiologie, Universi…

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

ADD COMMENT • link 10.0 years ago Simon Anders ★ 3.7k

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