[R] Discrepancy between R and SPSS in 2-way, repeated measures ANOVA

From: Larry A Sonna <larry_sonna_at_hotmail.com>
Date: Sat 10 Sep 2005 - 00:10:06 EST


Dear R community,

I am trying to resolve a discrepancy between the way SPSS and R handle 2-way, repeated measures ANOVA.

An experiment was performed in which samples were drawn before and after treatment of four groups of subjects (control and disease states 1, 2 and 3). Each group contained five subjects. An experimental measurement was performed on each sample to yield a "signal". The before and after treatment signals for each subject were treated as repeated measures. We desire to obtain P values for disease state ("CONDITION"), and the interaction between signal over time and disease state ("CONDITION*TIME").

Using SPSS, the following output was obtained:

                      DF        SumSq (Type 3)    Mean Sq    F value     P=

COND              3                 42861            14287       3.645 
0.0355
TIME                1                     473               473       0.175 
0.681
COND*TIME     3                     975               325       0.120 
0.947
Error                16                43219             2701



By contrast, using the following R command:

summary(aov(SIGNAL~(COND+TIME+COND*TIME)+Error(EXPNO/COND), Type="III"))

the output was as follows:

                  Df     Sum Sq     Mean Sq     F value  Pr(>F)

COND          3          26516       8839      3.2517     0.03651 *

TIME            1            473         473      0.1739     0.67986

COND:TIME  3            975         325      0.1195     0.94785

Residuals     28        76107      2718



I don't understand why the two results are discrepant. In particular, I'm not sure why R is yielding 28 DF for the residuals whereas SPSS only yields 16. Can anyone help?

E-mail replies would be much appreciated. I can be reached at larry_sonna@yahoo.com and at larry_sonna@hotmail.com

Thanks in advance,

Larry Sonna



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