set scan. With the NPL cutoff of 2, several regions on chromosomes 2, 7, and 12 that were significant in the SNP full set scan were no longer significant in the SNP subset scan. We also noted that the effect of genotyping error on the linkage results was small for this particular data set, although potential genotyping errors seemed to increase the linkage signal slightly, which contradicted with the finding of John et al. [2], who suggested that removal of unlikely genotypes could increase the significance of nominal loci. The discrepancy may due to the different genotyping error rates in the two data sets. There were 1,295 microsatellite genotypes that were likely to be errors and were set missing with MERLIN's error checking algorithm. Among the 1,614 individuals and 315 microsatellites, there were a total of 353,015 genotypes, so the error rate for the microsatellite markers was estimated to be 0.367%. Similarly, there were 27,338 SNP genotypes that were likely to be errors and were set missing with MERLIN's error checking algorithm. The error rate for the SNPs was estimated to be 0.204% as among the 1,614 individuals and 10,081 SNPs, there were a total of 13,395,832 genotypes.
