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Robaina / pathwayEnrichment

Tools to perform a permutation-based cell pathway analysis
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Implement maxT pvalue correction #2

Open Robaina opened 1 year ago

Robaina commented 1 year ago

See:

  1. https://stats.stackexchange.com/questions/166510/controlling-fwer-using-minp-maxt-methods, report both permutation pvalue and corrected permutaton p-value

  2. https://mne.tools/stable/generated/mne.stats.permutation_t_test.html

Robaina commented 1 year ago

maxT doesn't work because there are very small pathways that are very likely to have a high representation in the shuffled cluster, thus the maxT distribution contains very large numbers and the corrected p-value is always very large. Perhaps try minP procedure instead?