You probably have an unbalanced design (different number of cases in the
different conditions defined by the crossing "fact1*fact2"). One possiblity
is to use the 'car' package and Anova to get "type III" sums of squares.
This is equivalent to pretending that there is no "unbalance".

Christophe Pallier

On 5/15/07, Anders Malmendal <anders@chem.au.dk> wrote:
>
> I am using R to make two-way ANOVA on a number of variables using
>
> g <- aov(var ~ fact1*fact2)
>
> where var is a matrix containing the variables.
> However the outcome seem to be dependent on the order of fact1 and fact2
> (i.e. fact2*fact1) gives a slightly (factor of 1.5) different result.
> Any ideas why this is?
>
> Thanks for any help
> Anders
>
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-- 
Christophe Pallier (http://www.pallier.org)

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