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 <gunter.berton at gene.com> > >> 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 <hnorpois at gmail.com> >> 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) 0.05614 0.16782 0.335 0.738 >>> rs7572685 0.49041 0.41437 1.183 0.237 >>> rs10520302 0.49269 0.43514 1.132 0.258 >>> 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 at 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 at 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