> On Jul 21, 2016, at 3:04 PM, Qinghua He via R-help <r-help@r-project.org>
> wrote:
>
> Using the same data, if I ran
> fit2
> <-glm(formula=AR~Age+LumA+LumB+HER2+Basal+Normal,family=binomial,data=RacComp1)summary(fit2)exp(coef(fit2))
> I obtained:
exp(coef(fit2))(Intercept) Age LumA LumB HER2
Basal Normal
0.24866935 1.00433781 0.10639937 0.31614001 0.08220685
20.25180956 NA
> while if I ran
>
> fit2
> <-glm(formula=AR~Age+LumA+LumB+Basal+Normal+HER2,family=binomial,data=RacComp1)summary(fit2)exp(coef(fit2))
> I obtained:
exp(coef(fit2)) (Intercept) Age LumA LumB Basal
Normal HER2
0.02044232 1.00433781 1.29428846 3.84566516 246.35185956
12.16443690 NA
>
> Essentially they're the same model - I just moved HER2 to the last. But the
> OR changed significantly. Can someone explain?
You have collinearity and one of your variables will be dropped as redundant.
Which one is dropped is determined by the order of the variable names in the
model formula.
> For the latter result, I don't even know how to interpret as all factors have
> OR>1 (except Intercept), how could that possible? Can I eliminate the effect
> of intercept?
In the first model (with the defaults of treatment contrasts) the Intercept is
actually an estimate for cases with LumA, LumB,Basal,Her2 all at their lowest
level and this not coincidentally also precisely defines your Normal variable.
They all (excepting Normal) have adverse impact in your study of AR whatever it
might be. If these various categories (which I suspect are breast cancer risk
predictors) are all distinct with no overlaps, then use this:
fit2 <-glm(formula=AR~Age+ Normal+ LumA+LumB+HER2+Basal+
0,family=binomial,data=RacComp1)
The results will probably be the same as your first model except that
Intercept's parameter will now be the parameter for Normal.
> Also, I cannot obtain OR for the last factor due to collinearity. However, I
> know others obtained OR for all factors for the same dataset. Can someone
> tell me how to obtain OR for all factors? All factors are categorical
> variables (i.e., 0 or 1).
> Thanks!
> Peter
> [[alternative HTML version deleted]]
>
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David Winsemius
Alameda, CA, USA
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