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Huge DF denominators for repeated measures ANOVAs with JMP 14

Jan 22, 2019 10:57 PM
(4369 views)

I used to run repeated measures ANOVAs with JMP 13 with no proglems. But now I got JMP 14 and ran an ANOVA with the same data and somehow got "4326" as a DF Den under "Test Denominator Synthesis". This used to be "42" with JMP 13, and ovbiously the new F ratio got so much larger. I do not think there is anything different I did (data, how to set up), other than I am now using JMP 14 instead of JMP 13, and I really do not know what to do.

Could anyone please let me know what I am missing?

Thank you!

15 REPLIES 15

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

We do not know much about the details of your data or analysis but the increase in the DF for the denominator suggests that you have fewer DF for the model. Are there either fewer terms or fewer levels of your predictors?

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

Thank you very much for your response.

I attach a file with some images. Hopefully they will give you more information.

The image 1 shows how I specified the model with JMP 14, and the image 2 shows the output I get now. I am 100% sure that I used the same data set and 99% sure (I can no longer run JMP 13 to verify) that I used the same model specifiction, but I used to get an output like the image 3.

I do not know why DF Den are so different between the two versions, and would like to know how I could revert back to the output I used to get with JMP 13. I would really appreciate your help. Thank you!

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

The fact that your results with JMP 13 exhibit fractional degrees of freedom for the denominator of the F-test suggests that you used REML to estimate the parameters and variances. REML is the default (and recommended) procedure so that makes sense. On the other hand, EMS is selected for the analysis done with JMP 14. Try using REML with JMP 14.

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

Thank you very much for your response.

I tried using REML, but the results are the same as the attached image.

I am wondering if you could try running my data. It would really help me if you could. I will attach my data set with the following message. Thank you!

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

I don't see the need to nest Subject within Disease. I verified that the results without nesting are identical.

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

Here is the data file attached.

>Thank you very much for your response.

>

>I tried using REML, but the results are the same as the attached image.

>

>I am wondering if you could try running my data. It would really help me if you could. I will attach >my data set with the following message. Thank you!

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

It would have been helpful if you had suppled the JMP data table. I had to restore the meta-data and the model in Fit Least Squares by hand.

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

I verified your results with JMP 14.

It appears to me that almost half of the terms, all higher-order interactions, may be removed from the model.

I am not surprised that there are 4326 degrees of freedom for the denominator (MSE) of the F-tests. You start with 4576 observations and your model contains 208 parameters. I do not understand how the DF could have been only 42 in the original analysis.

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Re: Huge DF denominators for repeated measures ANOVAs with JMP 14

Thank you again for the quick reply!

I am sorry about the Excel vs. JMP formats, and I can see that for REML (although it makes a difference for EMS), there is no need for nesting Subject within Disease.

But my original questions still stay:

1. Why are the outputs so different between JMP 13 and JMP 14? If you look at the Test Denominator Synthesis sections for both, the JMP 13 secion lists different DF Den's for different factors, while the JMP 14 section list just one number (4326) for all the factors except Disease (42). Also, the Denom MS Synthesis column lists different factor combinations for different factors for JMP 13 but just "Residual" for all the factors except Disease for JMP 14.

2. How could I revert back to the output I used to get with JMP 13? I would like to use the JMP 13 version, as it matches the results from SPSS and Unix-ranova.

Thank you again.

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