why NA coefficients
On Nov 8, 2011, at 1:19 AM, David Winsemius wrote:
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.)
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
>
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David Winsemius, MD
West Hartford, CT