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In order to estimate these quantities, we must compare the number of statistically significant linkage tests with the estimated number of truly null and truly alternative linkage tests.
Thus, approximately 103 true-positive trans-acting QTL are detected in the 5067 random single marker linkage tests.
For the 1206 linkage tests significant at LOD≥1.37, the FDR estimated by Storey's and Tibshirani's method was 0.026.
There were 157 linkages called significant at LOD≥1.37 among the 5067 random marker linkage tests, and the associated FDR was ≈0.342.
First, we estimated the proportion of truly null tests (denoted π0) and truly alternative tests (1−π0) across all 5067 single marker linkage tests performed at the marker closest to the locus of the gene in question.
The estimate of π0 for this set of tests is approximately 0.898, indicating that about 518/5067 of these single marker linkage tests at random loci detect true trans-acting QTL.
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Linkage testing is a less sensitive method of testing and requires a suitable family structure.
The significance was determined empirically, by running the linkage test on ten permuted datasets.
In this event pathway linkage testing is used rather than sequence analysis to identify an APC mutation.
We planned a linkage test of the PTPN22- 1858T allele RA hypothesis, restricted to RF+ RA patients.
The remaining loci were dissected into groups at increasing stringency levels of the linkage test (LOD values from 3 to 12).
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