[R] different outcomes of P values in SPSS and R

[Martin Teicher]

R usesType I sequential SS, not the default Type III marginal SS reported by SPSS.  There is a good blog post explaining this difference along with some interesting comments -- http://myowelt.blogspot.com/2008/05/obtaining-same-anova-results-in-r-as-in.html

Best Wishes,

Martin H. Teicher
Dept of Psychiatry
McLean Hospital / Harvard Medical School
Belmont MA 02478


On Aug 13, 2010, at 10:32 PM, Ben Bolker wrote:

> Leo Vorthoren <L.Vorthoren <at> nioo.knaw.nl> writes:
> 
>> I have been using generalized linear models in SPSS 18, in order to build
>> models and to calculate the P values. When I was building models in Excel
>> (using the intercept and Bs from SPSS), I noticed that the graphs differed
>> from my expectations. When I ran the dataset again in R, I got totally
>> different outcomes for both the P values as well as the Bs and the
>> intercepts. The outcomes of R seem much more likely to be the correct ones,
>> but I really cannot explain the differences.
> 
>  I appreciate/assume that you're asking on the off chance that someone
> else has tried something very similar and gone to the trouble of figuring
> out the differences between R's and SPSS's default setup, but you're
> unlikely to get an answer without more detailed information.
> 
>  My best guess is that SPSS and R are using different contrasts
> and/or different baseline levels.  R uses treatment contrasts by default,
> and assumes that the first (alphabetical) level of a factor is the
> baseline level.
> 
>  It's conceivable that you have a dataset where the results are
> numerically unstable and sensitive to small details in the algorithms
> used.
> 
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