Whats the meaning of False Positive Rate (FPR)?
The false positive rate (FPR) is the proportion of negative sites that are erroneously predicted as positive hits. Given a data set containing all of non-phosphorylation sites, the real FPR could be easily computed. However, precise calculation of FPR is unavailable due to lack of a “gold-standard” negative data set. Here we developed a simple and fast method to construct the near-negative data set and estimate the theoretically maximal FPRs. Firstly, we calculated the distributions of amino acids composition in six organisms, including S. cerevisiae, S. pombe, C. elegans , D. melanogaster, M. musculus, and H. sapiens. Then we randomly generated 10,000 PSP(7,7) peptides to construct a near-negative data set based on the real frequencies of twenty amino acids in eukaryotic proteomes. Although there were a few sites to be real hits, its proportion would be very small. The process was repeated twenty times and the average FPR was calculated by GPS 2.0 as the theoretically maximal FPR. Als
