Sorry if this is awkwardly worded...I'm not sure how else to describe my question.
I have 4 "experiments" containing 3 "duplicates" with 28 "runs" in each. Each run is a time series of 300 seconds. I need to compare experiments to each other to determine if there is a statistically significant difference in the experiments. Eg, I'd want to do an ANOVA process on the experiments with pairwise t-tests following.
Since my data is time series only on the run level and I'm comparing on the experiment level, do I need to be concerned about/correct for autocorrelation? If so, what's the best way to go about doing that?
Not sure if it matters/helps, I have about 100 variables but I need the comparison to be for each individual variable so this is functionally a univariate comparison.