Did you read the TukeyHSD help page? You chose to have one factor, so you cannot blame R for your own choice.

Do be very careful that you understand what these so-called post hoc tests do (and also what the main effect of a factor in the presence of an interaction means, for in R it is not the same as in SPSS).

[It really isn't fair to send UTF-8 mail, and the formatting has gone wrong en route to me (if it was ever right). Plain text and wrapped lines please.]

On Sun, 15 Jan 2006, Andrej Kastrin wrote:

Dear useRs,
I'm working on multiple comparison design on two factor (2 × 3 levels) ANOVA. 
Each of the tests I have tried (Tukey, multcomp package) seem to do only with 
one factor at a time.

fm1 <- aov(breaks ~ wool * tension, data = warpbreaks)tHSD <- TukeyHSD(fm1, 
"tension", ordered = FALSE)
$tension          diff       lwr        upr     p adjM-L -10.000000 -19.35342 
-0.6465793 0.0336262H-L -14.722222 -24.07564 -5.3688015 0.0011218H-M  -4.722222 
-14.07564  4.6311985 0.4474210
I'm interested in posthoc comparisons between various levels of factor 1 and 
various levels of factor 2, both at the same time.I know that is possible in 
SPSS, but... is there any R solution?
Cheers, Andrej
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Brian D. Ripley,                  [EMAIL PROTECTED]
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