Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

Table 2 Concordance of calls between batch compositions

Comparison		BC1 vs BC2	BC1 vs BC3	BC2 vs BC3
Successful Calls for Both	SNPs	134128046	134063768	134107787
	%	99.241	99.194	99.226
Concordant Calls (All)	SNPs	134109060	134036623	134095792
	%	99.986	99.980	99.991
Concordant Calls (Hom)	SNPs	98050788	97992008	98016851
	%	99.989	99.983	99.993
Concordant Calls (Het)	SNPs	36058272	36044165	36078941
	%	99.977	99.970	99.985

Successful calls for both: genotype successfully called in both of the compared experiments; Concordant calls (All): same genotype called in both of the compared experiments; Concordant calls (Hom): homozygous genotype called in both of the compared experiments; Concordant calls (Het): heterozygous genotype called in both of the compared experiments.

ISSN: 1471-2105