How are q-values for pearson correlation are calculated?

[dllahr]

This thread provides links to the methodology / underlying methods - that might explain the difference you’re seeing:

Details on methodology of “Two Class Comparison”

Would it be possible to include some details on the two class comparison custom analysis method? I assume it’s a two sample hypothesis test with some form of multiple hypothesis correction, but the exact method that is used would be useful for reporting and reproducibility. It’s a great tool overall though, really has sped up the process of working through a lot of datasets quickly.