Chunk #33 — Statistical Methodology for the Analysis of Association Trajectories — Identification of significant SNPs — Significant SNPs identified by thresholding p-values by false discovery rate
Specifically, the distribution of p-values from non-associated SNP-phenotype pairs should be uniform on the interval from 0 to 1, while the the distribution of p-values from associated SNP-phenotype pairs should be concentrated near 0. From the estimation of the occurrence of non-associated SNP-phenotype pairs, it is possible to estimate the occurrence of associated SNP-phenotype pairs, and determine the false discovery rate, sometimes called a q-value, as a function of thresholding at different p-values. As with any thresholding technique, choice of a threshold is arbitrary, and the correspondence between p-values and q-values for levels q < .05 and q < .01 are determined. This procedure is appropriate for the evaluation of all obtained p-values collectively, as the algorithm deals with correlated values appropriately. This provides information on a fine-grained time scale. (The part of the original algorithm in Storey and Tibshirani (2003) which estimates the proportion of the non-associated results was modified to deal more robustly with truncated p-value distributions when necessary, and provides a somewhat more conservative estimate than does the original).
