Hi, I have 2 datasets of au values, they were analysed with different analytical methods, dataset A has N=60 and dataset B has N =252.which hypothesis testing method can I use to test if the two datasets are significantly different from each other?
Welch's t-test is roboust to unequal sample sizes and can help you determine whether two groups are significantly different from each other. See the following link for more information:
http://daniellakens.blogspot.com/2015/01/always-use-welchs-t-test-instead-of.html#:~:text=If%20sample%20sizes%20in%20both,(often%200.05)%20alpha%20level.
If your 60 samples in dataset A were also analyzed in sample set B I would opt for restricting my analyses to the 60 samples that appeared in both datasets and perform a paired t-test instead.
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