Hello Mark,
Sorry for not replying sooner this is the first day I have had access to JMP since your response. I appreciate that matched pairs are based on the differences, seeing as my raw data has all of the responses in a single column and then a column defining which time point a row is and a second column defining whether the response is from treatment or control I am trying to get my head around how much pre processing of the data I will need to do before running the statistical comparisons.
I now have 3 different JMP examples of my data which will hopefully demonstrate the issue I am having a bit better.
Dummy 1 - Response data in single column and therefore matched pairs or manova are not possible. I have saved a fit least squares full factorial comparison of timepoint and treatment which gives me p values for T1Control v T0control and T1invervention v T0Intervention. However these are unpaired comparisons and not appropriate for my data set.
Dummy 2 - Response data split into 2 columns T0 and T1 with a 3rd column defining treatment type. I have saved a manova repeated measures which when I look at the within-subjects section I think I understand demonstrates a significant change from baseline across the whole data (treated and control together) and a significant difference between time effect for treated and control. But the data does not give me separate p values for control T1vsT0 and treated T1vsT0.
Dummy 3 - Response data split into 4 columns T0control, T1control, T0intervention, T1intervention. I have saved a matched pairs analysis using all 4 columns which gives me the separate paired analysis p values for control T1vsT0 and treated T1vsT0 but does not give me the anlysis of whether the mean difference T1-T0 is significantly different between intervention and control.
I am sure I am missing something blindingly obvious but what I am looking for is a way to get the difference in time effect between treated and control from the Dummy 2 manova and and the difference between timepoints for each treatment from Dummy 3 all in one set of analysis.
Hope this makes things a little clearer.