

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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