Repeated measures ANOVA with missing data

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Repeated measures ANOVA with missing data

Steve-41
Hey all,

Brief info about my dataset: Cell counts from histological samples of
liver tissue were taken for case and control patients.  Each patient was
supposed to get 3 readings done by a pathologist who counted the cells
(but some patients only had 2 readings done). Need to find out if patients
on the treatment had a higher/lower cell count than control patients.

I was deciding between running a repeated measures ANOVA. However, I hit a
snag with the latter model.  Since I have missing data (2 instead of 3
slides read) for half my patients, the model delets those cases from the
analysis.

Is there a way to take the missing data into consideration in the repeated
measures ANOVA?  Syntax is fine but I'm not well versed in Python.  Should
I use some other model (mixed model, perhaps)?  Or would it be fine to run
a t-test using the average counts of each patient (would avoid the whole 2
readings vs 3 reading issue)?

Thanks in advance.
-Steve

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Re: Repeated measures ANOVA with missing data

Swank, Paul R
You need to use a mixed model instead. This will make use of what data
is there (using maximum likelihood) and is much better with missing data
than GLM, which uses listwise deletion in repeated measures.

Paul R. Swank, Ph.D.
Professor and Director of Research
Children's Learning Institute
University of Texas Health Science Center - Houston

-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of
Steve
Sent: Thursday, June 19, 2008 6:35 PM
To: [hidden email]
Subject: Repeated measures ANOVA with missing data

Hey all,

Brief info about my dataset: Cell counts from histological samples of
liver tissue were taken for case and control patients.  Each patient was
supposed to get 3 readings done by a pathologist who counted the cells
(but some patients only had 2 readings done). Need to find out if
patients
on the treatment had a higher/lower cell count than control patients.

I was deciding between running a repeated measures ANOVA. However, I hit
a
snag with the latter model.  Since I have missing data (2 instead of 3
slides read) for half my patients, the model delets those cases from the
analysis.

Is there a way to take the missing data into consideration in the
repeated
measures ANOVA?  Syntax is fine but I'm not well versed in Python.
Should
I use some other model (mixed model, perhaps)?  Or would it be fine to
run
a t-test using the average counts of each patient (would avoid the whole
2
readings vs 3 reading issue)?

Thanks in advance.
-Steve

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Re: Repeated measures ANOVA with missing data

Reutter, Alex
Also note that in order to use MIXED, you'll need to restructure your dataset.  If you look at Help > Case Studies..., then Advanced > Linear Mixed Models > Using Linear Mixed Models to Analyze Repeated Measurements, there are instructions on how to restructure a file from variables to cases (i.e., originally set up for use in GLM Repeated Measures).

Cheers,
Alex

-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of Swank, Paul R
Sent: Friday, June 20, 2008 10:29 AM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

You need to use a mixed model instead. This will make use of what data
is there (using maximum likelihood) and is much better with missing data
than GLM, which uses listwise deletion in repeated measures.

Paul R. Swank, Ph.D.
Professor and Director of Research
Children's Learning Institute
University of Texas Health Science Center - Houston

-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of
Steve
Sent: Thursday, June 19, 2008 6:35 PM
To: [hidden email]
Subject: Repeated measures ANOVA with missing data

Hey all,

Brief info about my dataset: Cell counts from histological samples of
liver tissue were taken for case and control patients.  Each patient was
supposed to get 3 readings done by a pathologist who counted the cells
(but some patients only had 2 readings done). Need to find out if
patients
on the treatment had a higher/lower cell count than control patients.

I was deciding between running a repeated measures ANOVA. However, I hit
a
snag with the latter model.  Since I have missing data (2 instead of 3
slides read) for half my patients, the model delets those cases from the
analysis.

Is there a way to take the missing data into consideration in the
repeated
measures ANOVA?  Syntax is fine but I'm not well versed in Python.
Should
I use some other model (mixed model, perhaps)?  Or would it be fine to
run
a t-test using the average counts of each patient (would avoid the whole
2
readings vs 3 reading issue)?

Thanks in advance.
-Steve

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Re: Repeated measures ANOVA with missing data

Steve-41
In reply to this post by Steve-41
Thanks Paul, Alex and Sara,

I was afraid that I might have to use mixed models.  Also, thanks to both
Alex and Sara (whose emails didn't go to the list and I'm posting below)
for giving me the heads up on restructuring the dataset.  It was
originally structured for a linear analysis and I had restructured it for
the ANOVA... so it's back to drawing board. Thanks again for the tips.

-Steve


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Sara House wrote on Fri, Jun 20, 2008 at 9:13AM

Steve -

If you use a mixed model, you wouldn't lose all your cases with missing
values.  Instead, you would be able to use all cases that have data at a
particular time.  At the risk of sounding like Don Hedeker's personal
cheerleader (I've recommended his site on this list before), if you go to
http://tigger.uic.edu/~hedeker/ you'll find SPSS and SAS syntax to do
mixed-model analyses with continuous data, and SAS syntax for dichotomous
data.

BTW, does anyone know if there is a way to do mixed model analyses with
dichotomous data in SPSS?  I don't have access to SAS at work and I'm more
familiar with SPSS anyway.

Sara

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Sara House wrote on Fri, Jun 20, 2008 at 11:43 AM

Steve -

Oop, sorry, didn't realize my first email went only to you and not the
list.  You can ignore the question in my email.

Also, Alex is right that you'll want to restructure your file.  So instead
of:

ID      T1Meas      T2Meas     T3Meas
1       x           y          z
2 ...

You'll want a single measurement variable and then a time variable:

ID         Meas       Time
1            x             1
1            y             2
1            z             3
2    ...

Hope this helps!


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: Repeated measures ANOVA with missing data

francesca
In reply to this post by Steve-41
Hi,

your explanation is clear but I am having the same problem and I would need more details if possible.

I have understood that I will restructure my data with time points in each row. But..the groups? I also have two groups (case and control) and how will the groups be organized?

And then, how do I have to proceed to do the analysis?

Thank you

Francesca
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Re: Repeated measures ANOVA with missing data

Maguin, Eugene
Francesca, where does this come from? According to nabble, you are replying to the last post of a message originally posted in 2008. You're having problems, I understand that but what is/are the problems that you are having? Please describe them, what you've tried to do and how what you tried failed. It sounds like this is a pretty ordinary varstocases problem.
Gene Maguin





-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: Saturday, February 21, 2015 4:44 PM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

Hi,

your explanation is clear but I am having the same problem and I would need more details if possible.

I have understood that I will restructure my data with time points in each row. But..the groups? I also have two groups (case and control) and how will the groups be organized?

And then, how do I have to proceed to do the analysis?

Thank you

Francesca



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View this message in context: http://spssx-discussion.1045642.n5.nabble.com/Repeated-measures-ANOVA-with-missing-data-tp1082833p5728764.html
Sent from the SPSSX Discussion mailing list archive at Nabble.com.

=====================
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Re: Repeated measures ANOVA with missing data

francesca
Hi,

thank you very much for this.

I think I made a mistake as I posted my trouble in someone else's post.

I have problems because I need to perform a two way repeated measures ANOVA with SPSS but using the mixed model, since some data are missing and I therefore can't perform the classic one.

I have understood that I need to rearrange my data and have them ordered with the repeated measure in vertical. But I also have a "between" factor (I have two groups). If I put the time in vertical for each subject, how will I organize my groups? And once the table is ready, how do I perform the two way repeated measure using the mixed model? On internet I have only found instruction for the one way but it does not apply to my case.

I hope my explanation is clear enough?

It would be very nice if you couls have any suggestion on that

Thank you very much

Francesca

2015-02-23 15:32 GMT+00:00 Maguin, Eugene [via SPSSX Discussion] <[hidden email]>:
Francesca, where does this come from? According to nabble, you are replying to the last post of a message originally posted in 2008. You're having problems, I understand that but what is/are the problems that you are having? Please describe them, what you've tried to do and how what you tried failed. It sounds like this is a pretty ordinary varstocases problem.
Gene Maguin





-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: Saturday, February 21, 2015 4:44 PM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

Hi,

your explanation is clear but I am having the same problem and I would need more details if possible.

I have understood that I will restructure my data with time points in each row. But..the groups? I also have two groups (case and control) and how will the groups be organized?

And then, how do I have to proceed to do the analysis?

Thank you

Francesca



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View this message in context: http://spssx-discussion.1045642.n5.nabble.com/Repeated-measures-ANOVA-with-missing-data-tp1082833p5728764.html
Sent from the SPSSX Discussion mailing list archive at Nabble.com.

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Re: Repeated measures ANOVA with missing data

Joost van Ginkel

Dear Franceska,

 

Check this paper:

 

Van Ginkel, J.R. & Kroonenberg, P.M. (2014). Analysis of variance of multiply imputed data. Multivariate Behavioral Research, 49, 78-91.

 

This paper provides you the tools to carry out a repeated measures ANOVA in SPSS on multiply imputed data sets. It’s better than using the multilevel approach for handling the missing data because multiple imputation can also take into account dependence of the missing data on variables that are not included in your analysis.

 

Best,

 

Joost

 

From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: maandag 23 februari 2015 16:44
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

 

Hi,

 

thank you very much for this.

 

I think I made a mistake as I posted my trouble in someone else's post.

 

I have problems because I need to perform a two way repeated measures ANOVA with SPSS but using the mixed model, since some data are missing and I therefore can't perform the classic one.

 

I have understood that I need to rearrange my data and have them ordered with the repeated measure in vertical. But I also have a "between" factor (I have two groups). If I put the time in vertical for each subject, how will I organize my groups? And once the table is ready, how do I perform the two way repeated measure using the mixed model? On internet I have only found instruction for the one way but it does not apply to my case.

 

I hope my explanation is clear enough?

 

It would be very nice if you couls have any suggestion on that

 

Thank you very much

 

Francesca

 

2015-02-23 15:32 GMT+00:00 Maguin, Eugene [via SPSSX Discussion] <[hidden email]>:

Francesca, where does this come from? According to nabble, you are replying to the last post of a message originally posted in 2008. You're having problems, I understand that but what is/are the problems that you are having? Please describe them, what you've tried to do and how what you tried failed. It sounds like this is a pretty ordinary varstocases problem.
Gene Maguin





-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: Saturday, February 21, 2015 4:44 PM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

Hi,

your explanation is clear but I am having the same problem and I would need more details if possible.

I have understood that I will restructure my data with time points in each row. But..the groups? I also have two groups (case and control) and how will the groups be organized?

And then, how do I have to proceed to do the analysis?

Thank you

Francesca



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View this message in context: http://spssx-discussion.1045642.n5.nabble.com/Repeated-measures-ANOVA-with-missing-data-tp1082833p5728764.html
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View this message in context: Re: Repeated measures ANOVA with missing data
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Re: Repeated measures ANOVA with missing data

Maguin, Eugene
In reply to this post by francesca

Ok. So your data must look like this for a one between (group=A or B)-one within (time=1 or 2) ANOVA.

Gene Maguin

 

Id group time1 time2

11 A             3         7

12 B              .         5

13 A             2         .

14 B             4         3

And so on.

 

Varstocases make DV from time1 to time2/index=time.

 

The result should be:

Id group time DV

11 A             1     3

11 A             2     7

12 B              2     5

13 A             1      2

14 B             1     4

14 B             2     3

 

 

 

 

From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: Monday, February 23, 2015 10:44 AM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

 

Hi,

 

thank you very much for this.

 

I think I made a mistake as I posted my trouble in someone else's post.

 

I have problems because I need to perform a two way repeated measures ANOVA with SPSS but using the mixed model, since some data are missing and I therefore can't perform the classic one.

 

I have understood that I need to rearrange my data and have them ordered with the repeated measure in vertical. But I also have a "between" factor (I have two groups). If I put the time in vertical for each subject, how will I organize my groups? And once the table is ready, how do I perform the two way repeated measure using the mixed model? On internet I have only found instruction for the one way but it does not apply to my case.

 

I hope my explanation is clear enough?

 

It would be very nice if you couls have any suggestion on that

 

Thank you very much

 

Francesca

 

2015-02-23 15:32 GMT+00:00 Maguin, Eugene [via SPSSX Discussion] <[hidden email]>:

Francesca, where does this come from? According to nabble, you are replying to the last post of a message originally posted in 2008. You're having problems, I understand that but what is/are the problems that you are having? Please describe them, what you've tried to do and how what you tried failed. It sounds like this is a pretty ordinary varstocases problem.
Gene Maguin





-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of francesca
Sent: Saturday, February 21, 2015 4:44 PM
To: [hidden email]
Subject: Re: Repeated measures ANOVA with missing data

Hi,

your explanation is clear but I am having the same problem and I would need more details if possible.

I have understood that I will restructure my data with time points in each row. But..the groups? I also have two groups (case and control) and how will the groups be organized?

And then, how do I have to proceed to do the analysis?

Thank you

Francesca



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