 Same question continued, example more detailed/representative of what I am
trying to analyze (partially nested, with replicates). Say we are interested
in comparing gene expression in yellow versus red fruits, and cannot find
red bananas or yellow strawberries etc.

> targets
   sample  color      fruit
1       1 yellow     banana
2       2 yellow     banana
3       3 yellow     banana
4       4 yellow      lemon
5       5 yellow      lemon
6       6 yellow      lemon
7       7    red     cherry
8       8    red     cherry
9       9    red     cherry
10     10    red strawberry
11     11    red strawberry
12     12    red strawberry

Fruit is nested in color, with 3 (biological) replicates for each existing
combination of factors.

design<-model.matrix(~color/fruit)
design<-design[,apply(abs(design),2,sum)!=0]

> design
   (Intercept) coloryellow colorred:fruitcherry coloryellow:fruitlemon
1            1           1                    0                      0
2            1           1                    0                      0
3            1           1                    0                      0
4            1           1                    0                      1
5            1           1                    0                      1
6            1           1                    0                      1
7            1           0                    1                      0
8            1           0                    1                      0
9            1           0                    1                      0
10           1           0                    0                      0
11           1           0                    0                      0
12           1           0                    0                      0
   colorred:fruitstrawberry
1                         0
2                         0
3                         0
4                         0
5                         0
6                         0
7                         0
8                         0
9                         0
10                        1
11                        1
12                        1

> fit<-lmFit(eset, design)
Coefficients not estimable: colorred:fruitstrawberry
Warning message:
Partial NA coefficients for 54675 probe(s)

My question here is: what should be the contrast matrix for a statistically
sound contrast highlighting the "color" effect.

Thanks in advance for hints.

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