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Other / Re: Peak alignment with large dataset (over 2500 samples and growing)
With such a large dataset it is very likely to suffer from big intensity drift issues you'd need to fix. XCMS does not provide tools for that but the papers you list have some tools.
A few other observations:
- setting `minFraction` to 1/n is extremely aggressive. I assume you get a lot of features. `minSamples`/`minFraction` are critical for getting rid of false positives in the peak picking
- are you sure `bw` is right? That means you don't expect more than ~1/60=0.017 min retention time difference between all your samples. Setting that so low might also give you batch effects if you have retention time differences between batches.