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How do I align and subtract two data sets?

 I would like to subtract one data from the other to get an insertion loss. By insertion loss I mean that I am running (2) test cases, one control system and one with equipment in the line. I want to get the difference in signal amplitude between the two tests. Hence by inserting the equipment into the system, what is the loss of signal amplitude. Having the difference (and later the quotient) will let me conclude how the equipment affects the system at each source pulsation frequency. 

 
Is there a way to ensure I’m subtracting the correct amplitudes by linking them to the frequencies? 
 
Even if the vectors were the same length, there is some variability in the frequency data since it was taken manually from the tachometer. I can’t be sure that sample 2000 is the same frequency on one run as sample 2000 on the next run, or even that I get a value for that frequency. 

NOTE:-


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You may consider using the timeseries object in this case.
 
Run the below command in your MATLAB instance to access the release specific documentation on 'timeseries' object:
 
 
web(fullfile(docroot, 'matlab/ref/timeseries.html'))

For example.

% Associate the frequency with amplitude
>> ts1 = timeseries(mag',freq');

% Associate another frequency with amplitude
>> ts2 = timeseries(mag',freq'-0.02);

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