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 <gunter.berton@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@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@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
>

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