Chunk #29 — Results — Searches for chromosomal regions identified by clustered SNPs with nominally-significant case vs control differences in both African-American samples
However, 199 of 200 permutation trials did provide data that identifies as many chromosomal regions from permutated data as those identified by the real datasets. Thus, the null hypothesis that the chromosomal regions identified by both samples are identified based only on stochastic grounds was not nullified by permutation testing, in ways that suggest that structure in the data may have contributed to the known propensity for permutation testing to overestimate false discovery rates in the presence of such structure [28], [29].
