How can I calculate Sum of Squared Errors of two matrices of a different number of rows

I would like to calculate SSE of two matrices of a different number of rows without loosing data and so obtain a new matrix were each kolom represents the SSE. Is it possible to "expand" or "shrink" (or project) a matrix? The problem is that I want to compare two measurement sets that were taken during the same timespan but they have a different amount of rows. I also have the time when each measurement was done.
Thanks for your advice.
Joël

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