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How to do Paired T-Test with Before/After Data and Multiple Variables For Multiple Subjects

CompositeLemur6

Hello there,

I am doing a project where I need to compare morning and afternoon

protein concentrations for some 600 proteins in samples from 5 individuals. I am using JMP Pro 18 Student Edition to do this. Lately, I am attempting to perform a paired T-test for all the proteins' concentrations in the morning and afternoon for each subject (1-5). I am not quite sure how to organize the data to get the software to do what I want it to do, and am looking for some guidance. Any help would be appreciated, this is my first time using JMP and doing a comparison like this. Attached I have an example of what the data looks like. I am open to all suggestions, and thank you for taking the time to read this!

Screenshot 2025-09-01 131821.png

JMP Pro community.xlsx

Accepted answers

txnelson

You need to use the Matched Pairs platform

Analyze=>Specialized Modeling=>Matched Pairs

Use your Morining and Afternoon columns as your Y, Paired Response

Use your Subject Time column as the By variable

Go to

Help=>JMP Online Help=>Matched Pairs

To get documentation and examples

All comments

txnelson

Here is the structure of the data that I suggest. It will allow you to take advantage of using row exclusion and By group processing to get your Paired t-Tests using the Fit Y by X platform

CompositeLemur6

Thank you so much for the suggestion! How might I actually perform this paired t-test, stepwise, if you would be so kind as to help me? I am not quite sure where the variables would be assigned. No worries if you cannot, and thank you again.

txnelson

You need to use the Matched Pairs platform

Analyze=>Specialized Modeling=>Matched Pairs

Use your Morining and Afternoon columns as your Y, Paired Response

Use your Subject Time column as the By variable

Go to

Help=>JMP Online Help=>Matched Pairs

To get documentation and examples