Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

Class comparison toolMultivariate permutation test• In the multivariate setting (i.e., when testing many genesfor significance at the same time), ask the question:What p-value pcutoff should I use to guarantee that 90%of the time, I get less than P proportion of false positives(where P is specified by the user)?• To answer this question, we compute the permutationdistribution of the p-value pcutoffs for which we wouldget P proportion of false positives.• The output tells us how far down the list we would beable to go in order to be assured (with a certainconfidence) of getting less than P proportion of falsepositives.88