[R] glm - change offset to avoid NA?

[David Winsemius]

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]]
>>> 
>>> ______________________________________________
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>> 
>> 
>> 
>> --
>> 
>> 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