Probably too late answer. RMS could be calculated after elimination of artifact (using filter) from the onset to the end of the EMG burst for each pedal revolution. Onsets and offsets could be determined using a constant electric threshold (i.e. +/- 0.2mV). Then, you can average each RMS values to obtain one value for each 6 s sprint. And then normalised them from your first sprint value (100%).
I have calculated the mean RMS during each 6s sprint according to Mendezet al. (2007). Fatigue responses during repeated sprints matched for initial mechanical output. Medicine and science in sports and exercise, 39(12), 2219-2225.
Did you normalise your emg signal somehow? How did you calculate mean rms? Rms is typically a measure of signal power and is a single value... The term "mean rms" sounds like you used an rms function to perform a linear envelope (with a set data window length and step width) then determined the average value of the enveloped data...