Dear R users,
I want to run nested fixed-factor Anova in R on different experiments.
In this toy example I have 3 levels of the main factor x1 and 7 levels
of the nested factor z1
x1 and continuous response variable y1.
x1
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2
2 2 2 2
[38] 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
3 3 3 3
[75] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
z1
[1] 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3
3 3 3 3
[38] 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5
5 5 5 5
[75] 5 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 7.
When I run lm on using nested design anov1=lm(c(as.vector(y1))
~as.factor(x1)+ as.factor(x1)/as.factor(z1)) I get a warning
summary(anov1)
Coefficients: (14 not defined because of singularities). I get
interaction between factors that should not be included because of the
nested design.
Why R includes them? This is becomes a problem when you apply similar
concept to large datasets having, i.e. 100 and 500 main and nested
factor levels - the computations become prohibitively slow?
Many thanks for your help in advance!
Coefficients: (14 not defined because of singularities)
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.1759 0.3226 -0.545 0.5869
as.factor(x1)2 -0.1276 0.4473 -0.285 0.7762
as.factor(x1)3 0.6461 0.4785 1.350 0.1802
as.factor(x1)1:as.factor(z1)2 0.1049 0.4473 0.234 0.8151
as.factor(x1)2:as.factor(z1)2 NA NA NA NA
as.factor(x1)3:as.factor(z1)2 NA NA NA NA
as.factor(x1)1:as.factor(z1)3 NA NA NA NA
as.factor(x1)2:as.factor(z1)3 1.1520 0.4473 2.575 0.0116 *
as.factor(x1)3:as.factor(z1)3 NA NA NA NA
as.factor(x1)1:as.factor(z1)4 NA NA NA NA
as.factor(x1)2:as.factor(z1)4 NA NA NA NA
as.factor(x1)3:as.factor(z1)4 NA NA NA NA
as.factor(x1)1:as.factor(z1)5 NA NA NA NA
as.factor(x1)2:as.factor(z1)5 NA NA NA NA
as.factor(x1)3:as.factor(z1)5 -0.6841 0.4181 -1.636 0.1052
as.factor(x1)1:as.factor(z1)6 NA NA NA NA
as.factor(x1)2:as.factor(z1)6 NA NA NA NA
as.factor(x1)3:as.factor(z1)6 -0.6713 0.4562 -1.472 0.1445
as.factor(x1)1:as.factor(z1)7 NA NA NA NA
as.factor(x1)2:as.factor(z1)7 NA NA NA NA
as.factor(x1)3:as.factor(z1)7 NA NA NA NA
----------------------------------------------
Sergii Ivakhno
PhD student
Computational Biology Group
Cancer Research UK Cambridge Research Institute
Li Ka Shing Centre
Robinson Way
Cambridge CB2 0RE
England
+44 (0)1223 404293 (O)
+44 (0)1223 404128 (F)
http://www.compbio.group.cam.ac.uk <http://www.compbio.group.cam.ac.uk/>
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