Hi, In the latest TPP versions ProphetModels.pl now calculates uncertainty values for the FDRs (both prophet and decoy calculated), with the decoy FDR uncertainties displayed as error bars in the plots. I note that the uncertainty values are calculated with the formula:
$PP_decoy_uncert = sqrt($fdr_pp_decoy*(1-$fdr_pp_decoy)/$num_pos_pp); I wondered where this formula comes from? I came across a paper recently in which FDR uncertainty is modelled, leading to asymmetric confidence intervals for the FDR dependent on dataset size and number of decoy hits: Edward L. Huttlin, Adrian D. Hegeman, Amy C. Harms, and Michael R. Sussman Prediction of Error Associated with False-Positive Rate Determination for Peptide Identification in Large-Scale Proteomics Experiments Using a Combined Reverse and Forward Peptide Sequence Database Strategy J. Proteome Res., 2007, 6 (1), 392-398 Given the example in the paper, where at 1% FDR there were 35 decoy hits out of 3418 We have a pipeline incorporating some of the TPP software where I need to give users an assessment of the uncertainty in FDRs, and am trying to decide whether to pass through the ProphetModels values or use the Huttlin et. al. model. Many Thanks, Dave Trudgian --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
