I have 2 experimental groups, each with 3-5 biological replicates.

I want a statistical test that can compare parameter x between the two experimental groups.

Within each biological replicate I have ~2000-4000 cells that I want to factor into the analysis. How should I do this? Taking the mean for each biological replicate and performing a t test to compare the experimental groups seems inappropriate since the variance of the data is not accounted for. Similarly, factoring in all the data points and performing t tests between the groups seems inappropriate.

Any advice would be much appreciated.

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