Suppose when I write the results of a microarray experiment fit using limma to file. In doing this I decide to adjust the p-values using the BH method for adjusting the p-values. As I understand it, this method assesses the significance of a result assuming some prior rate of false discovery (type 1 error). I read the 1995 paper for the BH method but I am still confused on what exactly determines this rate? Is it done in a parametric way or non-paramterically?

Joseph Cornish
Post-Bac IRTA
NIAID EVPS


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