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

[Martin Teicher]

What your saying is true.  The sequential/marginal difference can account for the discrepancy in p values but not necessarily the coefficients.  One thing I've found that can lead to differences in coefficients and p values between R and SPSS is whether or not you specify that a variable is a factor (e.g., group2 <- factor(group) ).  

Marty Teicher

On Aug 13, 2010, at 10:58 PM, Ben Bolker wrote:

>  Yes, but ... the original poster said the coefficients differed too.
>  (The blog post
> you refer to deals with ANOVA (i.e. linear models) rather than GLMs (generalized
> linear models): it is true that the sequential/marginal
> distinction still applies, but I don't think that can be the *only*
> thing going on here.)
> 
> 
> On Fri, Aug 13, 2010 at 10:50 PM, Martin Teicher
> <martin_teicher at hms.harvard.edu> wrote:
>> 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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>> 
>>