Re: [R] glm - change offset to avoid NA?
On Jul 16, 2013, at 8:52 AM, Hermann Norpois wrote: > I did not think of something like "try". I thouht that there should always > be a value if I do a logistic regression but sometimes the values are far > from being meaningful. So there is a cut-off. That seems implausilbe. I think you are just seeing the effect of a random selection creating a data situation where the interaction term is aliased with the others, in which case `glm` will set the coefficient to NA. > My plan was to change the > cut-off. You said there was an "error", but you should have said that the results were unexpected. You can create an "error-condition" when this occurs with the `stop` function. And then do whatever remedial work is needed. -- David. > Thanks > Johannes > > > 2013/7/15 Bert Gunter > >> I think what you want is >> >> ?try ##or >> ?tryCatch >> >> ## The second is more flexible but slightly more complicated. >> >> to trap the error and perhaps refit the model without interaction? >> >> Cheers, >> Bert >> >> On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois >> wrote: >>> Hello, >>> >>> I use glm within a function testing for the appearence of the coexistence >>> of (minor allels in a subset of) snps. And then I extract the >>> Pr(>|z|)-value for the interaction. Principally it works but sometimes >> the >>> function stops because this "value for the interaction" is NA. For >>> instance, this is the case in the following example: >>> >>> lz <- glm(trait~rs7572685*rs10520302, data=mus, family=binomial) summary (lz) >>> ... >>> Coefficients: (1 not defined because of singularities) >>> Estimate Std. Error z value Pr(>|z|) >>> (Intercept) 0.056140.16782 0.3350.738 >>> rs7572685 0.490410.41437 1.1830.237 >>> rs105203020.492690.43514 1.1320.258 >>> rs7572685:rs10520302 NA NA NA NA >>> ... >>> >>> I would prefer some values instead of NA (though it does not make any >> sense >>> in terms of interpretation) for the sake of the smooth running of my >>> function. How is this done? I guess I have to change the offset but I >> dont >>> understand how. >>> Thanks >>> >>>[[alternative HTML version deleted]] >>> >>> __ >>> R-help@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> >> >> -- >> >> Bert Gunter >> Genentech Nonclinical Biostatistics >> >> Internal Contact Info: >> Phone: 467-7374 >> Website: >> >> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm >> > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm - change offset to avoid NA?
I did not think of something like "try". I thouht that there should always be a value if I do a logistic regression but sometimes the values are far from being meaningful. So there is a cut-off. My plan was to change the cut-off. Thanks Johannes 2013/7/15 Bert Gunter > I think what you want is > > ?try ##or > ?tryCatch > > ## The second is more flexible but slightly more complicated. > > to trap the error and perhaps refit the model without interaction? > > Cheers, > Bert > > On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois > wrote: > > Hello, > > > > I use glm within a function testing for the appearence of the coexistence > > of (minor allels in a subset of) snps. And then I extract the > > Pr(>|z|)-value for the interaction. Principally it works but sometimes > the > > function stops because this "value for the interaction" is NA. For > > instance, this is the case in the following example: > > > > lz <- glm(trait~rs7572685*rs10520302, data=mus, family=binomial) > >> summary (lz) > > ... > > Coefficients: (1 not defined because of singularities) > > Estimate Std. Error z value Pr(>|z|) > > (Intercept) 0.056140.16782 0.3350.738 > > rs7572685 0.490410.41437 1.1830.237 > > rs105203020.492690.43514 1.1320.258 > > rs7572685:rs10520302 NA NA NA NA > > ... > > > > I would prefer some values instead of NA (though it does not make any > sense > > in terms of interpretation) for the sake of the smooth running of my > > function. How is this done? I guess I have to change the offset but I > dont > > understand how. > > Thanks > > > > [[alternative HTML version deleted]] > > > > __ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > -- > > Bert Gunter > Genentech Nonclinical Biostatistics > > Internal Contact Info: > Phone: 467-7374 > Website: > > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm - change offset to avoid NA?
I think what you want is ?try ##or ?tryCatch ## The second is more flexible but slightly more complicated. to trap the error and perhaps refit the model without interaction? Cheers, Bert On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois wrote: > Hello, > > I use glm within a function testing for the appearence of the coexistence > of (minor allels in a subset of) snps. And then I extract the > Pr(>|z|)-value for the interaction. Principally it works but sometimes the > function stops because this "value for the interaction" is NA. For > instance, this is the case in the following example: > > lz <- glm(trait~rs7572685*rs10520302, data=mus, family=binomial) >> summary (lz) > ... > Coefficients: (1 not defined because of singularities) > Estimate Std. Error z value Pr(>|z|) > (Intercept) 0.056140.16782 0.3350.738 > rs7572685 0.490410.41437 1.1830.237 > rs105203020.492690.43514 1.1320.258 > rs7572685:rs10520302 NA NA NA NA > ... > > I would prefer some values instead of NA (though it does not make any sense > in terms of interpretation) for the sake of the smooth running of my > function. How is this done? I guess I have to change the offset but I dont > understand how. > Thanks > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
