[R] Why did TukeyHSD not work when I used it for post-hoc for 2way within-subjects anova?

From: Xiao He <praguewatermelon_at_gmail.com>
Date: Sun, 06 Jun 2010 10:18:55 -0700


Dear R people,

I have a couple of questions about post-doc analyses for 2 by 2 within subjects ANOVA. I conducted a psycholinguistic study that combined a 2 by 2 design and a latin square design. Specifically, I had 32 items each of which generated 4 conditions. Participants saw each of the 32 items only once: 8 in Condition A, 8 in B, 8 in C, and 8 in D. The table below serves as an example.

*Subject* *Factor1* *Factor2* *Condition* *ReadingTime* *Item* 1 A A A 238
Item1 1 A A A 369 Item5 1 A A A 494 Item9 *.* *.* *.* *.* *.* *.* *.* *.* *.
* *.* *.* *.* 1 B A C 294 Item22 1 B A C 694 Item26 *.* *.* *.* *.* *.* *.*
*.* *.* *.* *.* *.* *.* 8 A A A 334 Item3 8 A A A 366 Item7 *.* *.* *.* *.* *.* *.* *.* *.* *.* *.* *.* *.*

I did ANOVA by using the following
:
result.subject=aov(ReadingTime~Factor1*Factor2 + Error(Subject/(Factor1*Factor2)), data=data), AND result.item=aov(ReadingTime~Factor1*Factor2 + Error(Item/(Factor1*Factor2)), data=data).

Both both functions returned significances. Now I am confused as to what methods I should use to do post-hoc analysis and how to use them. I attempted TukeyHSD, but it gave me an error message as shown below. I am not sure how to apply TukeyHSD properly since the help file was not clear enough on that. So I wonder if you can tell me what went wrong with my function.

> TukeyHSD(result.subject, c('Factor1','Factor2'), ordered=TRUE)
Error in UseMethod("TukeyHSD") :
  no applicable method for 'TukeyHSD' applied to an object of class "c('aovlist', 'listof')"

Also, I I attempted *pairwise.t.test* by averaging each participant's reading times in each condition (see the table below) with *p* values adjusted with Bonferroni method (*e.g. *pairwise.t.test(y,group, "bonferroni", pair=TRUE)), . It gave me significant results. But I am not sure if it is a proper method to use (Sorry I know this is more of a statistics related problem). So I wonder if you can tell me if pairwise.t.test is a proper method. If not, what other functions might be useful for post-hoc analysis. Thank you in advance!!

*Subject* *Condition* *AvgRT* 1 A 210 2 A 309 . . . . . . 19 A 305 20 A 502 1 B 480 2 B 209 . . . . . . 19 B 400 20 B 270 . . . . . . 19 D 190 20 D 254

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