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

Table 1 Concordance of calls between batch sizes

Comparison		BS1 vs BS2	BS1 vs BS3	BS2 vs BS3
Successful Calls for Both	SNPs	134258764	134187584	134265847
	%	99.338	99.285	99.343
Concordant Calls (All)	SNPs	134248899	134187584	134253973
	%	99.993	99.986	99.991
Concordant Calls (Hom)	SNPs	98179772	98136394	98204063
	%	99.997	99.993	99.995
Concordant Calls (Het)	SNPs	36069127	36031744	36049910
	%	99.981	99.964	99.980

Successful calls for both: SNP genotypes 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