TABLE 2

Computation of the false discovery rate for granddaughter design analyses of variances across families

iTraitsChromosomeMarkerFP(i)E(i)FWERq
1Fat %14157.15710-810-510-510-5
2Fat %315.2950.000030.0250.0240.012
3Fat yield14154.1460.000090.0770.0740.026
4Protein %245.2790.000420.3780.3150.094
5Protein %384.2460.000910.8180.5590.163
6SCS2213.8190.001010.9070.5960.151
7SCS2224.5900.001241.1120.6710.159
8Fat %383.8800.001941.7340.8230.217
9Milk yield733.4660.002312.0680.8740.230
10SCS2314.2180.002422.1660.8850.217
• Seven milk production traits were analyzed for 128 markers in the U.S. Holstein population. i, number of null hypothesis ranked by descending P; SCS, somatic cell score ; Chromosome, bovine chromosome number; marker, anonymous designation of DNA-microsatellite; F, F-value for the effect of paternal marker allele nested within grandsire; P(i), probability of corresponding F-value; E(i), expected number of rejected true null hypotheses with rejection probability P(i), computed as 896P(i); FWER, experimentwise type I error rate, computed as the probability of rejecting at least one hypothesis assuming a Poisson distribution for the number of rejected hypotheses with an expectation of E(i); q, expected false discovery rate when rejecting i hypotheses = 896 P(i)/i.