We have a microarray analysis with 7 treatments (different genotypes) with 3
replicates each. We'd like to classify them into groups that are different
from each other (e.g., genotype 1 is different from genotypes 2-7 and/or
genotypes 2, 4, 6 are different from genotypes 1,3,5,7). One way to do this
is to use the TukeyHSD function in R. However, we have an Error term in our
anovas that we need to remove (replicate effects).

It appears that TukeyHSD cannot use an aov that has any error terms. Is this
true and is there a way around it? Also, does anyone know an efficient way
to adapt the output of the TukeyHSD into something that states how many
groups exist and how many genotypes fall into the different groups.

Other suggestions besides TukeyHSD are welcome.

Thank you,
Mara

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