why NA coefficients
On Nov 7, 2011, at 10:07 PM, array chip wrote:
Thanks David. The only category that has no cases is "treat 1-group 2":
with(test,table(treat,group))
group
treat 1 2
1 8 0
2 1 5
3 5 5
4 7 3
5 7 4
6 3 3
7 8 2
But why the coefficient for "treat 7-group 2" is not estimable?
Well, it had to omit one of them didn't it? (But I don't know why that level was chosen.)
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