Accuracy versus ADPs for CRLMM (orange) and BRLMM (purple). Drop rates between 0 and 10% are examined. (a) ADPs are plotted for 269 HapMap samples hybridized by Affymetrix on 100K chips (XBA and HIND). Only high-quality hybridization data, as defined by Affymetrix, are used in this plot. The gold standard is HapMap calls. (b) ADPs are plotted for first-pass data from 152 and 95 samples hybridized on the 500K chips (Nsp and Sty) from the Broad Institute and Affymetrix, respectively. Again, the gold standard is HapMap calls. (c) ADPs are plotted for the 32 and 16 high quality replicates hybridized on XBA and Nsp chips. The consensus of the 32 and 16 high quality replicate chips is considered the gold standard for each chip type. Separate gold standards are derived from each calling algorithm result. These data were generated from the Chakravarti Lab. (d) ADPs are plotted for the 30 high quality trios hybridized on XBA and Nsp chips. Accuracy for trios is defined as percent of SNP trios that are Mendelian consistent. The trios may not have any dropped calls. The data were generated from the Chakravarti Lab.
Lin et al. Genome Biology 2008 9:R63 doi:10.1186/gb-2008-9-4-r63