Search
Question: How to specify Q75 for locfunc in DESeq2 estimateSizeFactors ? (Michael Love)
0
gravatar for Schnell, Dan
3.1 years ago by
Schnell, Dan30
Schnell, Dan30 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]]
ADD COMMENTlink modified 3.1 years ago by Simon Anders3.3k • written 3.1 years ago by Schnell, Dan30
0
gravatar for Michael Love
3.1 years ago by
Michael Love12k
United States
Michael Love12k wrote:
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 COMMENTlink written 3.1 years ago by Michael Love12k
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 REPLYlink written 3.1 years ago by Schnell, Dan30
0
gravatar for Simon Anders
3.1 years ago by
Simon Anders3.3k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.3k wrote:
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 COMMENTlink written 3.1 years ago by Simon Anders3.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 277 users visited in the last hour