[R] why NA coefficients

[David Winsemius]

On Nov 8, 2011, at 12:36 PM, array chip wrote:

> Sure it does, but still struggling with what is going on...

Have you considered redefining the implicit base level for "treat" so  
it does not create the missing crossed-category?

 > test$treat2_ <- factor(test$treat, levels=c(2:7, 1) )
 > lm(y~treat2_*factor(group),test)

Call:
lm(formula = y ~ treat2_ * factor(group), data = test)

Coefficients:
             (Intercept)                 treat2_3                  
treat2_4
               0.9292256               -0.1470106                
-0.7047343
                treat2_5                 treat2_6                  
treat2_7
              -0.3579398               -0.4558269                
-0.5077571
                treat2_1           factor(group)2   
treat2_3:factor(group)2
              -0.4999820               -0.5466405                 
0.0135963
treat2_4:factor(group)2  treat2_5:factor(group)2   
treat2_6:factor(group)2
               1.0087628                0.4362479                 
0.5402821
treat2_7:factor(group)2  treat2_1:factor(group)2
               0.2087338                       NA

All the "group-less" coefficients are for group1 , so  now get a  
prediction for group=1:treat=2 == "Intercept", group=1:treat=3 , ....  
a total of 7 values.

And there are 6 predictions for group2.

The onus is obviously on you to check the predictions against the  
data. 'aggregate' is a good function for that purpose.


-- 
david.



>
> Thanks
>
> John
>
> From: David Winsemius <dwinsemius at comcast.net>
> To: David Winsemius <dwinsemius at comcast.net>
> Cc: array chip <arrayprofile at yahoo.com>; "r-help at r-project.org" <r-help at r-project.org 
> >
> Sent: Monday, November 7, 2011 10:27 PM
> Subject: Re: [R] why NA coefficients
>
> But this output suggests there may be alligators in the swamp:
>
> > predict(lmod, newdata=data.frame(treat=1, group=2))
>         1
> 0.09133691
> Warning message:
> In predict.lm(lmod, newdata = data.frame(treat = 1, group = 2)) :
>   prediction from a rank-deficient fit may be misleading
>
> --David.
> >
> > --David.
> >>
> >> Thanks
> >>
> >> John
> >>
> >>
> >> From: David Winsemius <dwinsemius at comcast.net>
> >> To: array chip <arrayprofile at yahoo.com>
> >> Cc: "r-help at r-project.org" <r-help at r-project.org>
> >> Sent: Monday, November 7, 2011 5:13 PM
> >> Subject: Re: [R] why NA coefficients
> >>
> >>
> >> On Nov 7, 2011, at 7:33 PM, array chip wrote:
> >>
> >> > Hi, I am trying to run ANOVA with an interaction term on 2  
> factors (treat has 7 levels, group has 2 levels). I found the  
> coefficient for the last interaction term is always 0, see attached  
> dataset and the code below:
> >> >
> >> >> test<-read.table("test.txt",sep='\t',header=T,row.names=NULL)
> >> >> lm(y~factor(treat)*factor(group),test)
> >> >
> >> > Call:
> >> > lm(formula = y ~ factor(treat) * factor(group), data = test)
> >> >
> >> > Coefficients:
> >> >                  (Intercept)                 
> factor(treat)2                factor(treat)3
> >> >                      0.429244                       
> 0.499982                      0.352971
> >> >                factor(treat)4                 
> factor(treat)5                factor(treat)6
> >> >                    -0.204752                       
> 0.142042                      0.044155
> >> >                factor(treat)7                factor(group)2   
> factor(treat)2:factor(group)2
> >> >                    -0.007775                       
> -0.337907                      -0.208734
> >> > factor(treat)3:factor(group)2  factor(treat)4:factor(group)2   
> factor(treat)5:factor(group)2
> >> >                    -0.195138                       
> 0.800029                      0.227514
> >> > factor(treat)6:factor(group)2  factor(treat)7:factor(group)2
> >> >                      0.331548                            NA
> >> >
> >> >
> >> > I guess this is due to model matrix being singular or  
> collinearity among the matrix columns? But I can't figure out how  
> the matrix is singular in this case? Can someone show me why this is  
> the case?
> >>
> >> Because you have no cases in one of the crossed categories.
> >>
> >> --David Winsemius, MD
> >> West Hartford, CT
> >>
> >>
> >>
> >
> > David Winsemius, MD
> > West Hartford, CT
> >
> > ______________________________________________
> > 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, MD
> West Hartford, CT
>
>
>

David Winsemius, MD
West Hartford, CT