Downsampling from 100Hz to 60 Hz
Are the samples adhering to Nyquist (properly pre filtered)?
If so, I would just resample to one common rate, prefereable &gt;= max(rate1, rate2). And align them in time. Check out MATLABs resample() function.
If the samples are not adhering to Nyquist, then you need to think about what they represent, how they are sampled and in what respect you need to compare them.