[R] Two-way ANOVA gives different results using anova(lm()) than doing it by hand

[Lars Bergemann]

Hey!

 

Could you please take a quick look at what I have done? Somehow I get wrong results using the anova(lm()) combination compared to doing a two way ANOVA by hand.

 

Running:

 

Data<-read.table("Data.txt");
g<-lm(ExM~S1*S2,Data);
anova(g);

 

Gives:

 

Analysis of Variance Table

Response: ExM
           Df Sum Sq Mean Sq F value    Pr(>F)    
S1          1 4.3679  4.3679 167.045 < 2.2e-16 ***
S2          1 0.9427  0.9427  36.053 8.236e-09 ***
S1:S2       1 0.3231  0.3231  12.357 0.0005371 ***
Residuals 212 5.5434  0.0261                      


I compared it to the work done by hand, ie calculated all the different square sums using sum() and tapply().

So I know that anova(lm()) gets the degrees of freedom equal two 1, 1, 1 and 212 when it should be 5, 5, 25 and 180. Also, the square sums are quite different ... I get 4.xx, 4.xx, 1.xx, 0.xx ... as you see, what anova(lm()) gets is different.

 

The data: S1 has 6 levels, so has S2. On average, each cell has 6 values, most cells have actually 6 values, and there are two of each: 5, 7, 4, 8 - so average 6.

 

Could you please help me, why it does not work with anova(lm())? I tried quite a few thinks found with Google, but it all gave me the same result as anova(lm()) ... 

 

Thanks a lot!

 

Lars

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