R help - Jul 2013 - glm - change offset to avoid NA?

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]]

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

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