[BioC] meaning of pfp in RankProd

Matthew McCormack mccormack at molbio.mgh.harvard.edu
Wed Jan 31 16:17:08 CET 2007


I was wondering if someone could help me clear up some confusion I have 
understanding pfp in the RankProd Package.
If topGene returns a list of 10 genes (from a data set containing 20,000 
genes), and the gene ranked 8 on the list has a pfp percentage false 
positive) of 0.5, then does that mean that the list of genes ranked 1-8 
have an estimated false positive rate of 0.04 ( 0.005 X 8 ), that is, 
0.04 genes on the list (ranks 1-8) are expected to be false positives, 
or does it mean that the false positive rate for that gene and all 
ranked above it (ranks 1-8)  is 100 (0.005 X 20,000); 100 on the list 
are expected to be false ? Or maybe I am missing it altogether ?

Matthew



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